Supplements and the Autoimmune Protocol

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One question nearly everyone asks when transitioning their diet is “Should I be taking any supplements while on the Autoimmune Protocol?”. Supplements are some of the most commonly-recommended additions to dietary and lifestyle modifications, with everyone from functional medicine physicians to internet-forum users recommending their patients and friends take them. It is important to note that while supplements can be very helpful to the healing process, often times they can be a hinderance, stall progress, and even cause flares. A lot of people think of supplements as harmless, natural compounds, unlikely to cause problems, while in reality they can be profoundly effective at affecting change, for either good or bad. Because of this, I think it is important to educate yourself about what is in your supplements and the reason why you are taking them.

In this article, I aim to give you an overview of what supplements are, the pros and cons of taking them, how to evaluate a supplement, and some basic recommendations.

What are supplements?

Supplements are usually (but not always) extracted vitamins, minerals, and other compounds that have nutritional qualities contained in a small, but concentrated dose. Often these compounds are isolated to their most basic structure, and are combined with fillers in a standardized dose to supplemented with the diet. Sometimes these compounds are combined (as in a multi-vitamin), sometimes they appear alone with just fillers, and other times they are composed of pure, whole-food derived ingredients (such as encapsulated freeze-dried herbs). The idea behind supplements is to provide the body with a source of nutrients or other compounds that are not available in the diet, or to provide the nutrient or compound at a dose that would be impossible to get through diet.

Do you need supplements on the Autoimmune Protocol?

One of the strongest arguments for the Autoimmune Protocol is that it is an incredibly nutrient-dense diet (the most nutrient dense diet I’ve ever come across, in fact, especially when a person is eating organ meats, fish, shellfish, and a variety of vegetables). Eating this way (or a real-foods, ancestral style diet also incorporating these foods) provides all the nutrients a person needs to thrive. Beyond that, the nutrient-density is so high that the body has extra raw materials in order to regenerate and restore, which is necessary when healing from the inflammation caused by autoimmunity and chronic illness.

That being said, a good diet is only as good as it is digested. It does not matter precisely what we are eating, if we are not digesting our food properly, those components will not be properly broken down and transported to the cells that need them. For instance, eating a ton of liver may not help a person deficient in iron unless they correct the condition of low stomach acid that inhibits the digestion of iron. Many people find that supporting their digestive process with supplements in the beginning of their healing journey is more helpful than blanket supplementation of nutrients. If you suspect digestive dysfunction is at the root of your nutrient deficiencies, it is important to work with a practitioner who can help you support this process, there is no one-size-fits-all approach.

Past digestion, there are a few other reasons why people would chose to take supplements while on the Autoimmune Protocol. Some people suffer from autoimmune diseases where nutritional requirements are well known (for instance, selenium and zinc for thyroid). This does not always mean that they need supplements–it may just mean that they should make a better effort to get those nutrients from food (in the above case I would recommend eating 3-5 servings a week of fish and shellfish).

Some people take supplements, especially glandulars and herbs, to try and manage inflammation, influence the immune system, and combat stress. While this can be incredibly effective for some people, it is like playing with fire for others (read my article on Th1 and Th2 dominance for more info). If you are going to go this route, I recommend working with a knowledgable practitioner instead of putting yourself on a protocol. For managing stress, I believe those of us with autoimmunity have a better (and safer!) response to lifestyle changes than taking supplements–if you are looking for tips, Susan Vennerholm has a great article on the topic here.

How do you evaluate a supplement before deciding to take one?

I’ve come up with a list of questions you can ask yourself or your provider before deciding to incorporate a supplement into your routine:

  • Who recommended this supplement to you? Was it your doctor or someone you met in an online forum? Be weary that there are people online who make their living off of recommending supplements to those who are sick.
  • What is the purpose for this supplement? Is it to correct a nutrient deficiency or is it to encourage the body to change in some way? If your adviser cannot tell you why it is necessary, this should be a red flag.
  • How long will you need to be on this supplement? Is it a short-term thing, or is it something you will always be dependent on?
  • Does this supplement contain immune stimulants? Reference this article for a list of herbs and compounds that everyone with autoimmunity should be cautious of. If it has a known effect of stimulating the immune system, be warned that it could impact you negatively.
  • Does this supplement have known side effects, drug interactions, or warnings?
  • Does this supplement contain ingredients that are non-AIP, or is it produced in a facility that is not allergen free? Check out this article for more information on this topic.
  • Does this supplement contain any fillers that are unsuitable or that you have a sensitivity to? Again, this article can be helpful here.
  • Is this a supplement you could avoid taking by eating more of a particular food or correcting a known digestive issue?

How do I introduce a supplement into my routine?

It is very important, when deciding to incorporate new supplements, to introduce them slowly, one at a time (much like a food reintroduction). Nothing is worse than coming home from an appointment with a new natural practitioner with a bag of supplements, to start them all the next day and feel terrible. If you introduce too many things at once and have a negative reaction, it is impossible to pinpoint which supplement is causing the problem.

What are some supplements everyone can benefit from?

As you can see from the above, I am hesitant to recommend supplements in addition to diet because of the many issues concerning them. That being said, there are a few supplements that tend to be low-risk, well tolerated, and where the benefits outweigh the negatives. Here is my short list of recommendations, in addition to focusing on nutrient density wherever you can!

  • Magnesium–Because modern farming practices have left our soils depleted, it is actually pretty difficult to get enough magnesium, even on a real-food or Autoimmune Protocol style diet. It isn’t because we aren’t eating enough magnesium-rich food, but because the nutrient isn’t there for the plants to access in the first place. My favorite type of magnesium is magnesium malate.
  • Fermented Cod Liver Oil–I consider this more of a real food supplement than a traditional supplement, because it is not refined or treated in any way. While the Omega-3 fats like EPA and DHA are important for managing inflammation, most fish oils on the market are heat treated and refined, rancidifying the fats (not good!). Those who do not wish to eat organ meats or seafood like to take this brand of FCLO to make up for those lost nutrients.
  • Probiotics–A lot of people find that adding in a high-quality probiotic goes a long way to accelerating their healing. After all–we are all trying to heal our guts! One thing to know, is that the same probiotic that works for one person can cause symptoms in another, so it is important to start slow and not get discouraged if one does not work for you. I like to rotate between this product which is a more traditional probiotic as well as this one which contains soil-based organisms.

I hope that this article has answered your questions about supplementation and the Autoimmune Protocol, and if anything, has convinced you that a nutrient dense diet and less, not more supplementation is the safer approach.

Have you found supplements to be helpful or harmful on your healing journey?

About Mickey Trescott

Mickey Trescott is a co-founder here at Autoimmune Wellness and a co-teacher of AIP Certified Coach. After recovering from her own struggle with both Celiac and Hashimoto’s disease, adrenal fatigue, and multiple vitamin deficiencies, Mickey started to write about her experience to share with others and help them realize they are not alone in their struggles. She has a Master's degree in Human Nutrition and Functional Nutrition, and is the author of three best-selling books--The Autoimmune Paleo Cookbook, The Autoimmune Wellness Handbook, and The Nutrient-Dense Kitchen. You can watch her AIP cooking demos by following her on Instagram.


  • Tara says

    I love this article! Thank you so much! I’ve been working with a Functional Medicine doctor who I love and follow AIP but still struggle with symptoms and have found I react to supplements. I feel so much better knowing it’s not just me:) I feel like everything I try sets me back. Thanks again!

    • Mickey Trescott says

      I am so happy you found it helpful! Wishing you luck.

  • Ute says

    Perfect timing, Mickey!
    I have dropped all but the essential (for me: p-5-p, zinc, magnesium, B12 spray, D3/K7 drops, probiotics) supplements a week ago in preparation for more blood tests because my health keeps deteriorating…. and suddenly realized yesterday that I feel better than I have felt in months and there is no discomfort in my digestive system! I will concentrate on supplementing my AIP diet to support gut healing and spend (even) more on high quality food rather than on a drawerful of fillers and binders…
    Thank you for all the links you have provided; you are going from strength to strength on your blog and I appreciate your honesty in sharing your experiences.

    • Mickey Trescott says

      So happy to hear! I’ve definitely been there before, taking a ton of supplements and then all of a sudden stopping and feeling a lot of relief. Wishing you the best!

  • Amber says

    Another helpful article from you, in addition to your Th1 and Th2 write up which was eye opening for me. I’ve experienced ups and downs with various supplements for years suspecting that something was wrong in my body. Most helpful for me are actually your recommendations! Probiotics, Magnesium, HCLw/pepsin and Coq10 have been amazing for me. Beta Glucans pushed me into a horrible flare before I knew that me problems were autoimmune! I don’t mess around anymore with supplements, they are more powerful than most think, especially for us with AI disease.

    • Mickey Trescott says

      I’m so happy you found it helpful Amber! Like I said, those basics are pretty safe for most folks and they tend to need them, even with a great diet. Wishing you wellness!


      • MiKayla says

        Hi Mickey, I’m new to the AIP diet and have been struggling to find supplements that don’t include corn derivatives. I noticed the Magnesium supplement you recommended has microcrystalline cellulose and magnesium stearate, which are supposedly corn derivatives. Is it ok you take a supplement with these ingredients as long as the bottle says “corn free”?

        • Mickey Trescott says

          Hi MiKayla! I actually don’t recommend any specifics because formulations change all the time. It is difficult to find supplements free from corn, but they are out there. You’ll need to do your own research to identify those products that will work with your eliminations. Good luck!

    • Areli says

      Hi Amber, where can you find all those supplements you are mentioning in your comment? That would a great help for myself. Thank you.

  • Kimber Briggs says

    Does anyone know anything about Lymphocytic Microscopic Colitis? It’s not the same as ulcerative colitis, or IBS or anything else, really, and not much is known about it. One book has been written about it. I was diagnosed last year and after being on an elimination autoimmune paleo diet I finally got some relief after a couple of months. Now it’s back. I’ve been staying gluten-free and mostly paleo (I use a small amount of dairy w/lactaid). I started taking a turmeric supplement, but it doesn’t seem to be helping. I take Culturelle every morning, but that doesn’t seem to be doing anything either. My bouts seem to be “random,” with nothing in particular setting it off. I’m beginning to think the paleo almond bread I eat every morning is aggravating it, but who knows. If anyone knows anything that might be helpful I’d appreciate it.

    • Malori says

      Kimber!! It might sound silly that I’m excited about your comment – but I was also diagnosed with lymphocytic colitis last year!! I have found very little info on it but have been doing my best to manage it on my own (since I refused to take the prescription Uceris my GI doc wanted me to take). I’m also going to FINALLY see a functional medicine MD next week to help iron out this and other issues too. Please please feel free to reach out to me! My email is malori,[email protected] – I’d love to chat with you on what’s worked for you and just talk with someone who understands what it’s like to deal with this disease. You are the first person I’ve run across who has it.

    • Mickey Trescott says

      Really happy you two connected! Kimber, in reply to your original comment I do think that if you haven’t already, trying a strict elimination diet may help you sort out additional foods (like potentially the almonds) that are causing you issues. Good luck!

    • Efrosini Alexopoulos says

      i have recently done a food sensitivity test and found that almonds were something that my body was, maybe still is, sensitive too so i have eliminated almonds from my diet.

    • Marsha says

      I realize it has been a few years, but have you found anything to help your LC? I was diagnosed a few months ago and have found very little information (or help from my doctors). I tried Budesonide, but couldn’t tolerate it. It made me so incredibly anxious…felt like I was going crazy! My GI doctor told me I would just have to take high doses of Pepto indefinitely. I also have Hashi’s, which is currently giving me issues too. Any information would be so appreciated!

    • Danielle Rofe says

      You might also want to try a Omega 3 oil supplement like Fermented Cod Liver Oil for its anti inflammatory properties.

  • Jenny says

    I totally agree – supplements are so individualized and more is definitely not always better. I struggled trying so many different supplements on my road to healing from Hashimoto’s and IBS until I found a nutritionist who offered the Spectracell Micronutrient Analysis. I highly, highly recommend this test to anyone who suspects they may have nutrient deficiencies (most of us do, even those without autoimmune diseases) or is interested in customizing their supplements on the road to healing.

    • Mickey Trescott says

      I’ve heard about the spectracell test but have never done it myself. I’m happy it has helped you navigate your deficiencies!

  • Cheryl says

    I have multiple food allergies and SIBO, so there are so many things I cannot eat. If it doesn’t cause diarrhea, it causes migraines, or sinusitis. I had food allergies to tomatoes, rice and beans which you don’t think of as being allergenic foods. If you could get food allergy tested that would help you know if that might be your problem, otherwise you need to keep a food diary and eat simply for a few days to narrow it down, as I know with me, it might take 3 days for something to bother me that I ate. I just recently had to give up my green smoothies. It’s either the bananas or the pineapple.

    • RW says

      Im not sure what is in your green smoothies but spinach and kale RAW can do more harm than good to a person who had immune problems, Often, genetics are a factor. We can’t process certain foods when genetics are at play. I was doing green smoothies and they were knocking me out, making me feel weak and tired. I stopped the smoothies, I got better. That’s when I read that cruciferous foods are dangerous to a poorly functioning adrenal system. Now, you could try COOKING the greens, first. Alternatively try dandelion greens. Looking at the fruits, if your body is not breaking down the fruits (often a cause of methylation malfunctions), you’ll have lots of problems, too. A person who studies genes, biology, and Western and Asian Medicine can help you get on track if they do a genetics test to see where your genetics come into play, Some dietary changes and supplements help to heal your inflammation and allow your body to function more normally.

  • Stephanie says

    This is a great article to keep people informed about supplementation. I think it is dangerous for people to put themselves on a protocol. It is definitely something that should be done with a knowledgeable practitioner. That being said, I don’t like fish and cannot bring myself to do organ meats so I have to supplement with high quality fish oil and I have recently tried selenium and zinc. I have Hashimoto’s and still just don’t feel great. Struggling to get sugar out of my life and still having issue with gut healing. I saw a practitioner that put me on a gut healing supplement and basically an AIP diet (minus organ meats and fish) and I found I did well, my digestion was better. He took me off the plan because my tests all came back good. I had a naturopath tell me that my lack of energy was because of emotional stress or lack of emotional well being (she may have been partially right but there is something else going on that I just can’t figure out). So I do think you are right that people should get their nutrients from food but that is not always going to happen. Eating AIP takes a lot of prep and planning and people sometimes fall off the wagon. 🙂 Also, why do you like the magnesium malate? I take a magnesium 5-oxo-proline & saccharomyces cerevisae var. magnesium that also has thiamin, B6, L-glutathione and Taurine in it. What about Natural Calm?

    • Mickey Trescott says

      Hi Stephanie,
      I like magnesium malate because it is better absorbed and affects the muscles more than citrate (which also tends to produce loose stools for a lot of people). Natural calm is magnesium citrate. I don’t think it is bad, but if I am going to recommend a supplement and take it myself, I’d rather absorb than throw my money away!

  • apelila says

    There has to be a better way to get Omega 3 than the overpriced FLCO. Does anyone know of legit research and testing on fish oil supplements? The cost of wild caught fish is as bad as the FLCO, and one can only tolerate so much liver.

    • Mickey Trescott says

      If you think about what they are doing–extracting oil from the liver of fish, no wonder it is so expensive. If you can’t afford the supplement or the fish, I’d make sure to eat grass-fed and pastured meats (which has far more omega-3 fats) and possibly limit intake of omega-6 fats (like poultry fat and nuts). Hope it helps!

  • Meagan Faeth says

    Hi Micky,
    Thank you for this article! So many of my function medicine prescribed supplements (specifically the liquid ones from Apex Energetics) contain Xanthan Gum…. And one even includes Gur Gum as part of the “proprietary blend” !! Should i be pushing him to find other sources do you think? Or should I quit worrying and assume the good outweighs the the bad? (He has trained under Dr. K)

    • Mickey Trescott says

      It is absolutely possible to ask for your practitioner to look for supplements that don’t contain thickeners or fillers you react to. While I have worked with some great functional docs trained by Dr. K, the Apex line of supplements is not very autoimmune-friendly. WAY too many ingredients and lots of fillers. When I work with my doc, I ask her for the ingredient she is looking for (i.e. instead of an adrenal multi, we will try just rhodiola) and then find my own clean version of that.

      Hope it helps!

      • Loretta says

        Mickey, just curious. Which Functional Doctor or Practitioner(s) do you work with, personally?

        • Mickey Trescott says

          Loretta, I don’t share that information publicly.

  • Jessie says

    I have been on AIP since March. I am really wanting to get on a prenatal supplement but the one that I really like and took my last pregnancy is not AIP compliant. It is Garden of Life’s RAW prenatal and it has nightshades and rice hull in it. Do you have any suggestions? I have Hashimoto’s and my symptoms have been improving greatly on AIP despite my blood work not getting better (actually looks worse on paper). I just tried the Rainbow Light prenatal which appears to have no triggers in it but I got a sore throat which I haven’t had since I eliminated everything from my diet. :/ I would appreciate any advice.

    • Mickey Trescott says

      Hi Jessie,
      I would definitely look for another prenatal that does not contain rice and nightshades. Unfortunately I don’t have a specific recommendation because I don’t usually work with multivitamins. Maybe you can ask your practitioner about supplementing with a few necessary, high-quality nutrients instead of a multi?

      • Sarah says

        Hi Mickey, I take Vitamin c and zinc as well. I’m trying to get off my plaquenil which is at the moment making me worse but I’m trying to boost my immune system (I have lupus diagnosed 10 months ago) do u think vitamin c and zinc are ok?

        • Mickey Trescott says

          Hi Sarah,
          I can’t give specific recommendations without having a client relationship, but generally vitamin C and zinc are helpful and well tolerated. I would make sure to examine fillers to make sure there aren’t any non-AIP fillers lurking in there. Good luck!

        • Mr Antony Arcuri says

          Is your vitamin C ascorbic acid? If so it’s derived from corn which as I understand is a none paleo food.

  • […] Find more recipes from @mickeytrescott on her Instagram feed and […]

  • […] Trescott, who co-blogs with Angie Alt at Autoimmune Paleo, has a post about how to evaluate supplements, including probiotics, when on a healing […]

  • […] Supplements and the Autoimmune Protocol – Autoimmune Paleo […]

  • Emily says

    Hey there!
    I was just wondering if there are any AIP approved fish oil capsules available! I’m really worried I won’t be able to handle the un-capsulated version!


    • Mickey Trescott says

      Hi Emily!
      We don’t make specific recommendations, but I would look for a brand that uses minimal cold-processing and doesn’t have any other fillers if you do chose to take fish oil. I would recommend getting cold water, fatty fish in your diet regularly as an alternative!

  • Kelly says

    I think I just accidentally posted this on a different post on your site, but meant for it to be here…Hi, I have Hashimoto’s and just recently began the AIP diet. I have stopped taking my New Chapter postnatal multivitamin, but continue to take Thorne vitamin d3/k2 drops as well as New Chapter Wholemega fish oil. My concern is that I am breastfeeding and in addition have lost weight since beginning a gluten/sugar free diet a few months ago and now even more weight loss in the first week of AIP. This is not a good thing for me because I barely weigh 100lbs now and I already appeared slightly underweight before cutting my diet. I am now reacting (dermititis) to coconut in any form which is what I have depended on for fat and calories. Are there any additional supplements that I should take due to breastfeeding and what foods should I focus on eating to gain weight since coconut oil is out? I do eat avocado pretty regularly as well as fatty meat as much as possible.

    • Mickey Trescott says

      Hi Kelly!
      Unfortunately we can’t answer medical or supplement questions, but about the weight loss, I would suggest trying to eat lots of starchy carbs (sweet potato, plantain, taro, yuca) and use them as a vehicle for fat (olive oil, duck fat, tallow, lard are all options that might work for you). Hope it helps!

  • Kaycee says

    This article fails to help the average individual because it refers back to working with a practitioner. It’s true, people do have so many negative symptoms they have put themselves under their own protocol from perusing the internet and procuring what they learned into treatment in the best way they know how. Practioners are terrific but the challenge for many is they don’t accept insurance and their rates are easily often in the thousands to get anywhere in their trial and error program with their supplements, making their services cost prohibitive. Except, of course, for those who are wealthy enough. Very dissapointing.

    • Mickey Trescott says

      Hi Kaycee,
      It is actually illegal, not to mention not helpful to folks, for me, as a nutritional therapy practitioner to make blanket recommendations without knowing a person’s history and background. This stuff is highly individual, and I have no way of knowing if a person is on a medication or has a health condition that is contraindicated or if that supplement will make them sick. Many health insurance plans these days have allowances for naturopathy and/or integrative docs. It is not easy to work with this broken system, but for the resourceful it can be done.

  • Annika says


    i would love to know what you think about supplementing Vitamin E on the AIP Diet. As far as i know, the AIP Diet is very low on Vitamin E, and i have Neurodermatitis and autoimmune Urtikaria. The doctors i have been seen have not been very helpful (except of giving me cortison). And i actually read that Vitamin E can be very helpful for skin conditions.

    Thank you & best wishes from Germany 🙂

    • Mickey Trescott says

      Hi Annika,
      No issues with supplementing with E, as long as you can find a soy-free and otherwise AIP variety!

  • Lauren says

    Thanks for the great post. I have hashimoto’s and just started on AIP (day 4!). I’m a little confused about the ingredients of some supplements that I’d like to continue taking (anti-candida, digestive enzymes, probiotics). Do any of the following ingredients raise any alarm bells?

    Microcrystalline cellulose, magnesium stearate, silica, milk thistle seed extract, oregon grape root extract, oregon grape root, grapefruit seed extract?

    Any advice is greatly appreciated!

    • Mickey Trescott says

      Hey Lauren!
      I can’t make specific nutritional or supplement recommendations without seeing a history, but as far a the AIP is concerned I think those ingredients are likely fine. Cellulose can irritate some people with sensitive guts, but is fine for most. Some of those ingredients have antibiotic propertie (like GSE) and I would say should be used under the care of a practitioner and not taken long-term. Hope it helps!

  • Gaye Bennett says

    I have a peculiar auto-immune situation which does not allow me to supplement with D3. When I attempt this my kidneys suffer even if I put it on my skin hoping it will absorb. I attempted a UV narrowband B light and that resulted in an eruption of bullous pemphigoid. I am considering trying a natural food source of Cod Liver Oil. Any suggestions? Thank you

    • Mickey Trescott says

      Hi Gaye! I think this question would be best addressed by a medical practitioner who is knowledgable about this complex issue. Do you have the same reaction when you get sunlight exposure on your skin? I do think having good guidance here would be helpful in your situation. Wishing you luck!

  • Silvia says

    Hi ! Which form of zinc or zinc brand do you recommend ? AIP compliant of course 🙂 I cannot eat seafood because it´s not avaliable where I live and I have a lack …thank you so much..

    • Mickey Trescott says

      Hi Silvia! There are many zinc brands on Amazon, I don’t have one in particular that I recommend but it shouldn’t be hard to find one without any non-AIP fillers. About the seafood – have you considered ordering frozen online and having it delivered to your home? Many companies, like Vital Choice, offer this! Good luck.

  • Zvonimir says

    I am from Croatia and I am following your blog. I think it s great. I have MS and I am on AIP. I need just some information. What do you think about rhodiola-adaptogen (of course 100%), and can I take this while I am on AIP? It s clear about aswagandha because is nightshade than is not allowed but rhodiola? I am asking because of stress managemet?!
    Thank you for answer.

    • Mickey Trescott says

      Hi Zvonimir! Ashwaganda is not included on the elimination diet, but rhodiola is one adaptogen many have a good experience with since it is not immune stimulating. Hope it helps!

  • Kathi Bergstrom says

    Hi, I’m considering trying the AIP diet, right now I am gathering information about what is allowed and what is not allowed.

    First: I usually make my own milk kefir but I know dairy products are not allowed so I’m converting my grains to make coconut milk kefir. I have been experimenting making my own coconut milk and have been using a vegetable glycerin as a emulsifier. Then I noticed that my vegetable glycerin is made from soy, so that is out. If I find a vegetable glycerin that is not made from soy, would that be allowable?

    Second: I grow and dry my own stevia from seed, is it okay to use the dried, unprocessed leaves in herbal infusions as sweetener?

    Third: what about other homemade herbal infusions for asthma and allergies, these are also made with alcohol but are used in very small amounts, like drops at a time.

    If I’m going to do this diet I want to do it right.
    Any input you have is appreciated.


    • Kathi Bergstrom says

      Sorry, I have one more: what about Maca root? I believe it is in the same family as turnips and cabbage so I assume it is okay, just want to check.

      • Mickey Trescott says

        Hi Kathi, Maca is a no because it is an immune stimulant.

    • Mickey Trescott says

      Hi Kathi! Great questions. Glycerine is out because it is usually either made from corn or soy, both of which are out on the elimination diet. So is stevia, even if it is the fresh herb (you can try reintroducing this in stage I if you like). I make coconut milk without thickeners all the time, just plain coconut flakes, water, and a little sea salt. Your herbal infusions should be fine at that dose if you choose to continue them or use occasionally, but make sure the herbs are not immune-stimulating (like echinacea, ashwaganda, etc.) as these are to be avoided on the elimination diet. Good luck!

  • cathy says

    I just started the AIP protocol, but I need to take vitamin E because my organic acid test suggested that I am in a dire need of antioxidants, and Vitamin E has been recommended: however, most Vitamin E are made with soy or vegetable oil so I know these ingredient are out. I found one that is made with annatto. Is this allowed?

    • Mickey Trescott says

      Hi Cathy, anatto comes from a seed so not technically AIP, but some folks make supplementation decisions including some reintroduction ingredients because the benefit of healing outweighs the potential negative reaction they may have. Hope it helps!

    • Cathy Hilbert says

      Thank you, but I have another question concerning cacao butter. Is cacao butter allowed? I use it to make white chocolate, but I stopped because I am not sure if it is allowed.

      • Mickey Trescott says

        Cathy, it is not included in the elimination diet.

  • Margo says

    I was wondering if Plexus is AIP Paleo approved?

  • Eric says

    Your probiotic has corn starch in it.

    • Mickey Trescott says

      Eric, I am aware VSL changed their formulation to contain corn last year.

  • Marianne Espasa says

    Hi !

    I was wondering if fillers such as magnesium stearate, silica, gelatin, microcrystalline cellulose, hypromellose, hydroxypropyl de methyl cellulose, talc could be an issue for us ? Most supplements have these, and even if they are not a grain, or a legume, or dairy, maybe they could be harmful ? What do you think ?

  • Traci Veno says

    Hi Mickey,
    Thank you for the article. I would like to get everything from only food but I am worried about getting enough balanced omegas. How much fish do you recommend if I do NOT supplement with a fish oil (a rough estimate is fine) and I am eating beef liver on a regular bases (your recipe and I love it hehe) I also just started with sardines a few times a week. I know it is hard to answer because everyone is so different in their health.
    Any help you can give is so much appreciated!!

    • Mickey Trescott says

      Hey Traci! I think if you are eating seafood 5-7 times a week, you would be doing GREAT on your omega balance. If you have to eat conventionally-raised meats (especially poultry) you might want to have more seafood, especially the cold water, fatty fish in the mix. If you are eating all grass-fed and pastured, you might be able to get away with 3-5 times a week. As you guessed, it is highly individual, but some people feel best when they include either a lot of seafood, or supplement with fish oil. I’m not against supplements in all cases, but most people can do to prioritize eating that high-quality seafood because it comes with a lot of other nutrients!

      • Traci Veno says

        Thank you Mickey! You’re the best! In a few weeks it’s strawberry picking at the farms around Portland Oregon. So you two come see us xo
        Kind Regards,
        Traci Veno

  • Fran says

    Hi Mickey,

    So basically no seeds in any form. Correct?

    • Mickey Trescott says

      Hi Fran, yes if you are on the elimination phase of the autoimmune protocol, no seeds or their derivatives.

  • Hi Mickey! I was diagnosed with fibromyalgia in my 20’s and Sjögrens this past April. I developed terrible peripheral neuropathy in both feet after a plantar fasciotomy on my left foot on September 2016. When I found out I had Sjögrens, and found it was autoimmune I began reseraching. I dove full in to the AIP diet! About a week ago I started a horrible flare and my peripheral neuropathy came back horriblg

    • It submitted before I was done haha. Story made shorter, I started on a vitamin regimen recently and realized the vitamins contained MANY things o wasn’t supposed to have. Soy, guar gum starches, etc! Do you believe I’m right in assuming this is what’s caused me to slide backwards? The AIP diet was like a miracle to me. No inflammation, no drugs!

      • Mickey Trescott says

        Hey Lorri! I’m so sorry that happened to you, and I can’t say for sure, but it could be a factor in your flare… or not. Even after experiencing success on AIP, a lot of people with autoimmune disease find they have the occasional flare. It could also have been stress, or lifestyle induced… at any rate, I hope you are feeling better, that you’ve got your supplements cleaned up, and back on track! Good luck!

  • Ava says

    Hi, when I switched from SAD to a nutrient dense Whole30/wahls version of the AIP, my digestive problems got worse. I started experiencing some pains in my upper abdomen and a lot more bloating/gas. I also sometimes had very soft, almost diarrhea-like stools, which were sometimes greasy. I go to a conventional doctor because there are no functional medicine doctors near me. I’m wondering what would be good functional medicine tests to order online to find out what may be going on. Also, do you know if people who take stomach acid and digestive enzyme supplements are supposed to take them for life or are they supposed to be able to get off them? If they’re supposed to get off them, how should they transition off? Thanks for your wonderful resource!

    • Mickey Trescott says

      Hi Ava, it sounds like you transitioned to a diet higher in fat content before your body was used to it – what you are describing sounds like the digestive consequences of eating too much fat too soon. If you do see a functional doctor, I would ask them to look into supporting your gallbladder and fat digestion, perhaps with ox bile, or lipase. Another idea would be to lower your fat intake and increase more slowly. Hope it helps!

  • Chris says

    Hi Mickey!

    I just a have a quick question regarding Nightshades and AIP – so I have severe Adrenal Fatigue, and have been taking a natural form of Vitamin C for it, but I find the price per dose way too high. I found another Vitamin C with almost 5 times as much Vitamin C per dose at a cheaper price (same quality), but included in the “Organic Blend” of Fruits and Vegetables has Organic Green Bell Peppers and Organic Tomato. The blend totals at 720mg altogether, which includes like 20-30 other AIP safe ingredients. My question is – would this be alright to take still while going full AIP or does even minute amounts like this matter?

    Thanks in advance!

    • Mickey Trescott says

      Hey Chris! Personally, I would not take a supplement with even the smallest amount of nightshade content while in the elimination phase. This is a very common sensitivity for folks, and it would be a pity to derail your progress over that little amount. Hope it helps!

  • Jenna S. says

    Hi, thank you for for writing this article, Ive found it to be very helpful. I have a question regarding Maca, is it compliant with aip? Ive tried searching online but havent found too much regarding hashimotos in particular.

    • Mickey Trescott says

      Hey Jenna, Maca is a supplement to be cautious of because it can have immune stimulating properties.

  • Katie says

    HI! I am looking forward to beginning the AIP soon to help heal my colon from ulcerative colitis! I want to start taking VSL3. I know it now contains cornstarch. Is this a supplement you still recommend?

    • Mickey Trescott says

      Hi Katie! I used to recommend it before they switched to a formulation with corn. If you have done reintroductions and know you are alright with corn it might be a good option for you, but I might try a different brand that doesn’t have a non-AIP filler. I’ve used Gut Pro with good success. Hope it helps!

  • Cevie Toure says

    Hello, I am Iron Deficient and I am on my 4th day of AIP. I am wondering if you know much about a supplement called Iron Response by Innate Response Formulas and is it AIP friendly.
    Thanks you.

    • Mickey Trescott says

      Hi Cevie! I’m not familiar with that supplement, but most of us in the AIP community who have had issues with iron like to include organ meats (like liver!) to keep our stores up. Personally I find it to work better than a supplement. Hope it helps!

      • NCG says

        Hi Mickey
        I’m totally new to AIP and I’m getting some infos to start online and at the AIP summit.
        But I have some issues with iron and to know if it’s the lack of stomach acidity or whatever I checked on my iron-intake…
        If I would eat about 100g of beef liver (that wouldn’t be good though I guess because the vitamin A per day would be way more than the limit of 25000IU and I can’t afford to buy that much oyster to make up for the copper) that would be only about 38% (Cronometer) of the daily recommendation… I think I miss something…
        And wouldn’t be octopus perhaps the better option for me? Or which vegetables (I eat a lot of spinach with vitamin C everyday, but still…) should I focus on?
        Find it really difficult to get my had wrapped up on some nutrient-issues… Sorry if my question is silly… But checking with cronometer I seem not able to find the balance of nutrients and some advice would be muuuuch appreciated…!
        Thank you so much for your work, it’s really helping me! <3

        • Mickey Trescott says

          Hi NCG! First, I commend you for taking nutrient density so seriously… I love that you are really digging deep into the foods you are eating and acknowledging your digestive impact. That being said, the data on cronometer should not be taken as precise… not only do they not know the actual nutrition contained in the foods you are eating, they also aren’t able to estimate what is appropriate for YOU (yes, your hight and weight is not enough information!). So, I would take the information with a grain of salt. If you are looking to really dial things in, working with a nutrition professional who can take a look at your history and what you are eating to make sure you are in the clear, that might be really helpful (we have a great listing over at For iron, I would focus on getting a variety of heme-iron sources (like red meat, especially organ meats) and then also consider boosting digestion and making sure you are eating iron-rich foods with cofactors like vitamin C. I would not assume you have an iron deficiency if you are not seeing physical symptoms or have normal blood work (your doctor can help you evaluate this). It is hard to dig in any further without more specifics, but I think in general it sounds like you are doing a great job at thinking about nutrient density, and as long as you are eating red meat, focusing on digestion, and especially including organ meats you should be on the right track (barring any medical reason why you might need a higher intake of iron, which a practitioner could help you with).

  • Brynn says

    As far as probiotics, should I take VSL#3 while on the AIP since it contains cornstarch? I’m having a very hard time finding a potent probiotic that is AIP compliant, and I noticed that you recommended VSL3 (as did my doctor). How do I navigate this while avoiding these foods?

    • Mickey Trescott says

      Hey Brynn! VSL #3 recently changed their formulation – the old product didn’t include cornstarch. Now I recommend Klare labs as theirs are allergen-free.

      • Kelly says

        Thank you for the recommendation of Klare Labs for their allergen-free probiotic. When visiting their website, I was overwhelmed with the variety of choices. Is there are certain one that you would recommend starting? I am starting an AIP diet and have an auto-immune disease.

        • Mickey Trescott says

          Hi Kelly! I am happy you found that connection helpful. Unfortunately I can’t make a specific recommendation as it really depends on your specific history. Tolerating probiotics is very individual and sometimes you might need to try a couple different varieties to determine what works best for you!

  • Mary W says


    Your website has been such a huge help to me during my healing process from GI issues caused by Celiac and SIBO and a permeable intestine. I have been on the AIP diet now for a few weeks and have really enjoyed a lot of your recipes I have found here and have seen improvement with my GI issues. I am also using supplements I have researched well for support (things like l-glutamine, magnesium, zinc, etc the list goes on). I was interested in adaptagens due to my stress response and anxiety issues. I found ashwaghanda is a no no because it is a night shade. And I did see rhodiola and holy basil are ok.

    I was wondering your take on schisandra. Is schisandra AIP friendly?


    • Mickey Trescott says

      Hi Mary! To be honest, I am not sure about schisandra, as I am not very familiar about it. I would say if it has any immune-stimulating properties, it should be avoided.

  • Julie says

    Thanks for this article! Can you recommend brands of vitamins and supplements that are AIP compliant? The search has been overwhelming! My daughter gets most of her nutrients through diet, but a few supplements have been suggested…the issue is finding GF, nightshade free brands. Thanks for any suggestions of brands.

    • Mickey Trescott says

      Hi Julie! I know how overwhelming it is! Unfortunately we don’t keep a list because manufacturers change their formulations so often that we don’t want to be responsible for any issues. The best thing you can do is start with brands you already know work out of a GF facility and then scan ingredients on a product-by-product basis. I’ve never found a brand that has supplements that are 100% AIP – it is usually one thing from one brand, and another from a different one. Maybe someone will start an AIP supplement line and save us the headache someday!

  • Norah says

    Any chance you can update the link for the suggested probiotics? The links no longer work. :/

  • Sandra says

    Same questions for me – would love to find out which probiotics you recommend as I’d like to start taking supplements for my autoimmune condition. Thank you!

    • Mickey Trescott says

      Hi Sandra! I don’t recommend any specific probiotic across the board. In my nutrition coaching practice I make the selection based on the information I gather during my intake process. Everyone has individual needs and tolerances, and I take this into account when making personalized recommendations. My best advice is to see how you feel trying different AIP compliant products and stick with the ones that produce the best effects. Good luck!

    • I was wondering if you could share the probiotics you use that are aip elimination phase compliant. The links in the article above no longer work and the name of the probiotic supplement is not spelled out. Thank you!

      • Mickey Trescott says

        Hello! I no longer take probiotics, so I don’t have a recommendation for you. Sorry!

  • Cheryl says

    Hi Mickey,

    I’ve been trying to find a sublingual B12 that is AIP friendly but everything I come across has natural flavors, vegetable glycerin, stevia, etc. Do you know of any brands that are okay on AIP or should I just take a capsule and be done with it? Thank you! Been a fan and follower for years.

    • Mickey Trescott says

      Hi Cheryl! Is there a reason why you think you need the supplemental B12? An AIP diet is very plentiful in this nutrient, especially if you are eating enough organ meat. I am not aware of any clean supplements because I haven’t needed to recommend them to my clients eating this way.

  • Sylvia says

    I just reviewed the newer comments and I see that you don’t recommend a specific brand anymore. No need to answer my previous question. Sylvia

  • Kathy says

    Not eating nuts, beans and grains. Isn’t there some minerals that I am missing out on when doing the AIP?

    • Mickey Trescott says

      Hi Kathy! As long as you are eating animal foods and leafy greens, I don’t think you’ll be missing any minerals.

  • Lindsay Ripplinger says

    Hi Mickey, I’m about to start AIP in a couple of weeks (working on transitioning right now). I take Biosil, a vegan collagen supplement where the main ingredients are: Silicon (as Choline-Stabilized Orthosilicic Acid) (ch-OSA), Choline (as ch-OSA), Microcrystalline Cellulose, Purified Water, Capsule Shell (consists of Hydroxyproply MethylCellulose).

    I have been taking this for about a year for joint pain and I believe it has been helping somewhat. Do you know if those elements are AIP-compliant, or would I be better to integrate bone broth and natural grass fed beef collagen instead? Thank you, your books have been very informative and are giving me the confidence I need to begin this journey.

    • Mickey Trescott says

      Hi Lindsay! Unfortunately I can’t give specific supplement recommendations without a history, but if it is collagen you are looking to add I would suggest using plain collagen (I’ve used Great Lakes and Vital Proteins brands with success). That way you get less fillers than come in the product you mention. You can also up your intake of broth and cuts of meat with more connective tissue in them (like rump roast!). Hope it helps!

  • Loretta Peters Martin says

    Mickey, is Moringa AIP compliant?

    • Mickey Trescott says

      Hi Loretta, Yes moringa is AIP, but be cautious with any plants used in a medicinal way as sometimes folks react to them in therapeutic doses.

  • Leslie says

    Thank you for this! I am working to find AIP compliant probiotic capsules. The links you posted don’t seem to be working anymore. Could you re-link those or give brand names? THANK YOU!!!!

  • Leslie says

    Never mind my last comment! I followed your suggestion re Klaire labs for a probiotic

  • […] on my own hygiene, I clean more – from the nearly constant cooking, I kind of need to- I supplement more regularly, and I even find that my self-soothing has improved. The latter has been pretty […]

  • […] I clean more – from the nearly constant cooking, I kind of need to- I supplement more regularly, and I even find that my self-soothing has improved. The latter has […]

  • Caroline Collins says

    Hey there!

    The links for the probiotics are dead, can you tell me what you recommend? I’m making my way to incorporating more fermented foods but for the time being, I’m still adjusting to the diet and I’m not sure I can add in making fermented foods to better my gut health just yet.

    Thank you!

    • Mickey Trescott says

      Hi Caroline! I don’t link to specific products I take anymore because supplements are so individual and what works for me might not work for others.

  • Charlie Q says

    Just wondering whether collagen or glutamine would be a worthy supplement to aid healing?

    • Mickey Trescott says

      Hey Charlie! I don’t think they are necessary – I always encourage folks to include food sources of collagen and glutamine (hello – bone broth!) before considering a supplement. That being said, a lot of people like to take them to boost gut-healing effects. It is up to you!

  • Kelley says

    Hello, 🙂

    Neither of the two links for probiotic products on Amazon are working.
    Could you please reply with the names of the two probiotics you like?
    I need to buy some as soon as possible.
    I appreciate you!


    • Mickey Trescott says

      Hi Kelley! I don’t make general recommendations for any supplements, even probiotics. My suggestion is to try some different formulations to see what works best for your gut, as everyone’s experiences and needs are different!

  • Stephanie says

    Thank you so much for all of your articles and everything u do! It’s all been very helpful. I’m curious if I should take glutathione while in the elimination phase of AIP? I assume it causes an immune response and thus I should t take it, but I don’t know. Any help is appreciated. I have searched and searched for answers before asking here.

    • Mickey Trescott says

      Hi Stephanie! Unfortunately we can’t advise on specific supplements because we are not medical providers. This is something you should run by your doctor. I know some folks use glutathione, but I have no way of knowing if it would be appropriate for you. Good luck!

  • Alexandra says

    Hi Mickey! Can you please update the links for probiotics, because they’re not valid anymore. Thank you!

    • Mickey Trescott says

      Alexandra, I don’t provide specific recommendations anymore, especially for probiotics, as they can be so individual.

  • Sara says

    Hi Mickey, I still need several supplements due to my disability; more B12 for brain health, D/K because I can’t go outside, and DHA for retinal lattice degeneration (fish oil has more EPA). I strive to buy the purest whole food supplements, but there’s always some AIP forbidden ingredient. Are these things legal in supplements: wheatgrass, barley grass and alfalfa grass, spirulina and chlorella, cellulose/hpmc capsules, vegetable glycerin, potassium sorbate, citric acid (derived from citrus fruits), inulin/fos, trace amounts of milk and soy (in probiotics), alcohol as a preservative, and castor bean oil.

    Other questions: Are herbal teas (skullcap) allowed or just green and black teas? How do you get enough fiber without grains? Wouldn’t the same goals be accomplished by eating nothing but sprouted pseudo grains, legumes, nuts and seeds?

    I started eating no more than one chicken breast a week thirty years ago. I became a vegetarian twenty years ago and then a vegan fifteen years ago. Probably not coincidentally, I’ve also had MS for 26 years. I know you were a vegan too (as was Dr. Wahls), but I just can’t make myself eat an animal. As I told Michele from Thriving on Paleo, I would rather die (and probably will) than eat an animal. I also question the effectiveness of the AIP diet for the more life threatening autoimmune conditions. What’s your take? Thanks!

    • Mickey Trescott says

      Hi Sarah! To your question about supplements – many of the ingredients you listed are not AIP-legal, and could pose a problem for someone with specific food allergies or sensitivities (like corn, soy, or dairy). It is really up to you whether or not you include them. To the vegan issue, I have come to understand that even animals have to die in order to produce plants (fertilizer is made from the byproducts of the meat industry, and truly “veganic” produce fails to thrive). I no longer believe that humans can remove themselves from the circle of life. If you want to know my thoughts on AIP & vegetarianism/veganism, read this article:

      • Sara says

        Thanks, Mickey:

        I’m sorry I bothered you about the supplements. I found the answer for most of them after I posted my question. Will you just please tell me your opinion on glutamine?

        I appreciate your article as you make a lot of good points. I just know too much about animal slaughter to get the images out of my head. Fish gasping for breath, lobsters being plunged into boiling water, cattle bleeding out, live chickens hung upside down on conveyor belts. Don’t get me started on the cruelty of conventional farming. Even my cat gets free-range chicken! Bottom line, it isn’t the fault of these poor sentient souls that I have MS.


        • Mickey Trescott says

          Hi Sara! A lot of people in the AIP community take L-glutamine. I know it can have side-effects for some people, especially in higher doses. I prefer to get it in the form of bone broth.

  • Louise says

    Is Green Pasture’s cinnamon FCLO AIP-compliant or just the unflavored version? Does the AIP diet allow their FCLO/Concentrated Butter Oil Blend (per Dr. Weston A. Price)?

    • Mickey Trescott says

      Hi Louise! I’m not familiar with those specific ingredients, but cinnamon is AIP elimination-phase friendly, and butter is not. Hope it helps!

      • Louise says

        Just to follow up… Green Pasture uses beeswax for their capsules. Is beeswax AIP-friendly when used this way? Do you recommend also taking regular fish oil for the Omega-3s? Thank you!

  • Golden says

    Can you please update the Amazon links for the probiotics? They are are dead links. Or maybe the brands? Most seem to have gums, maltodextrin or potato starch in them. Thanks!

    • Mickey Trescott says

      Hi Golden! I don’t recommend any products specifically as formulations change. I suggest reaching out to an AIP Certified Coach to help make personalized supplement recommendations:

  • Stephanie says

    Is either acacia gum or rice allowed when used as excipients in supplements? What about milk and soy in probiotics? What do you suggest for fiber since psyllium is off the table? Thank you.

    • Mickey Trescott says

      Hi Stephanie! These ingredients are not considered AIP, but if you are working with a provider who has determined the risk of the supplement causing an issue is lower than the potential benefit, you might include it. I recommend seeking out a coach to guide you here:

  • Bridget says

    The probiotic links in this article are no longer good. Is there an updated article or link for aip safe probiotic products?

    Thank you!

    • Mickey Trescott says

      Hi Bridget! Unfortunately probiotics are changing all the time, and I recommend working with a provider who can make a specific recommendation for you. You’ll find a listing of AIP Certified Coaches here:

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