A Practical Guide To Fermented Foods For Autoimmune Disease (Guest Post by Sarah Ramsden)

This post contains affiliate links. Click here to see what that means!

In order to support our blogging activities, we may receive monetary compensation or other types or remuneration for our endorsement, recommendation, testimonial, and/or link to any products or services from this blog.

That being said, we only promote authors, products, and services that we wholeheartedly stand by!



I’m taking a break from blogging this summer as I focus on my move, but in the meantime I have some great guest posts on various topics lined up from the autoimmune community. This post is by Sarah Ramsden.

Changing your diet and lifestyle to address an autoimmune condition, can be nothing short of overwhelming. You need to start paying attention to thinks you never considered before, like your sleep, spending time outdoors, and really addressing stress. You can’t eat many of your old favorites, and for the true healing effects of food, you have to add in things that you’d never in a million years consider otherwise. For me, that was fermented foods.

The week I was diagnosed with the autoimmune condition multiple sclerosis, I was also told I had a brain tumour called a meningioma. In a matter of weeks I was under the knife having brain surgery, which led to 3 months off work to recover, and the rest of the year slowly adding in pieces of my life until I was running at full steam again. Only then did I have the mental space to start thinking about MS.

A life long reliance on medication didn’t appeal to me, and I looked elsewhere for answers. That’s when I discovered the concept of going grain free, which led to paleo, and then the autoimmune protocol. The fermented foods came last, and I tentatively added them to my own plate several years ago through necessity. I’ll be honest, the idea frightened me a little (adding bacteria to my food?!), but they won me over with their delicious flavour.

While the research into the role specific bacterial strains play in our body is on-going, we do know that eating fermented foods on a regular basis is beneficial when addressing autoimmune disease. A healing addition to your diet, they are involved in immune modulation; fighting infection; speeding the healing process; have anti-inflammatory effects; and provide digestive benefits such as improving the integrity of the gut mucosal barrier, and helping to correct gut dysbiosis (an imbalance in gut bacteria).

Today I’m going to pass on some tips around the practicalities of fermented foods and autoimmunity that I’ve learned not only from my personal experience, but also from working with clients in my nutrition practice.

Getting started with fermented foods:

If you are new to fermented foods, start by choosing something familiar to you, there’s no need to make it more intimidating than it needs to be! I was a pickle addict as a kid so that’s where I started. If you used to love sauerkraut on your hot dog then that’s your sweet spot, or if you have a thing for fizzy drinks try kombucha. There’s no right or wrong place to start as long as the ingredients fall within what you can tolerate on the autoimmune protocol.

Buy raw and unpasteurized:

Unfortunately, the majority of “fermented foods” found in mainstream grocery stores are completely lacking in the beneficial bacteria and yeasts that make them so healthy. In order to maintain a consistent texture and flavour, the majority of brands pasteurize their products to make them shelf stable, and this process kills the health-promoting nature of the product.

In some of these shelf stable “ferments” such as pickled cucumbers and onions, the standard is now to use vinegar as a preserver rather than the traditional brine used in fermentation. Add pasteurization to the mix, and again you’re not getting the beneficial effects you might expect. The rule is, that if something is on the shelf, it’s been pasteurized. If it’s in the fridge, it’s typically unpasteurized. You can double check by looking for raw and unpasteurized on the label.

Read the ingredients:

As with anything, it’s still important to read ingredients. Not only will you avoid ingredients that might disagree with you, like mustard seeds in pickles, or fennel seeds in sauerkraut, but you’ll also get a second confirmation of the raw and unpasteurized nature of the product. In vegetable based ferments you’re looking for simple ingredients like  “water, vegetables, salt”, and in the case of something like kombucha you want to see “water, sugar, tea, culture”. If there’s another form of sweetener at the end of the list, you know it has been sweetened after the fermentation process, an unnecessary step and best avoided by you.

Variety is key:

Once you’re comfortable with your first ferment, start introducing new ones. Just as variety is important in your diet to make sure you get a full spectrum of nutrients, a variety of ferments will also diversify the bacteria you’re exposed to. There’s a huge number to choose from that are AIP compliant, for example there’s sauerkraut, lacto-fermented vegetables like carrots, broccoli, cauliflower, sweet potatoes and pickled cucumbers, beet kvass, fermented fruit, kombucha, and water kefir.

Quantity and frequency:

Fermented foods aren’t a quick fix, but bring positive changes with consistent use. When you start eating fermented foods, start slowly; maybe a ¼ cup of fermented vegetables, or half a cup of kombucha for instance. I recommend to my clients with autoimmune conditions, that they aim to eat or drink a ferment daily, ideally with every meal. My personal approach is to have a glass of kombucha with breakfast, and sauerkraut or some kind of lacto-fermented vegetable (cauliflower is my favorite) with lunch and dinner.

Dealing with symptoms:

Like any dietary introduction, pay attention to any symptoms that may result, looking for signs of digestive distress, fatigue, anxiety, depression, mood changes, or a flare up of skin issues. If you do experience symptoms, the first thing to do is to rule out a sensitivity to an ingredient in the ferment as opposed to the fermented nature of the food. So if you eat sauerkraut and experience bloating, double check that cabbage, or cruciferous vegetables in general aren’t the issue. Then you can determine that it’s the addition of the bacteria and yeasts that are the root cause of your symptoms. Most commonly, this is the result of an imbalance in gut bacteria called dysbiosis.

Once symptoms have subsided, reduce your serving size and try again. If you find you’re particularly sensitive, don’t underestimate the positive effect of even a very small amount of fermented food or drink. Some people can only tolerate a spoonful of sauerkraut juice to begin with, and then slowly graduate up to adding in the vegetable, and later increasing quantity and frequency.

People who should be cautious:

Those of you with a histamine sensitivity will have problems with many fermented foods, but before you give up, try kombucha which is known to be better tolerated. Likewise, if you have a yeast sensitivity, you may have to rely on probiotic supplements because while fermented foods are known for their beneficial bacteria, they also contain beneficial yeasts that can cause a reaction.

Take care of your microbiome:

While our digestive system holds the majority of the bacteria in our body, we are literally covered in them, from our skin, to our eyes, to in our noses, mouths, and in women, the vagina. There are literally 10 times the number of them, than there are our own cells! An overall approach to taking care of these guys, who mutually take care of you, involves a variety of steps. Firstly, if you’re doing AIP you’re already eating a wide variety of vegetables that influence the health of your friendly bacteria.

Next, remove all anti-microbial cleaners, soaps and supplies from your home. Instead you can replace them with all natural soaps, solutions like Norwex Microfibre Cloths, and probiotic products like PIP Perfect Skin Hygiene Spray. It goes without saying that you should be very selective in your antibiotic use.

Finally, get outdoors and get dirty; do some gardening, play with your kids in the sandbox, and get regular contact with animals, whether they be pets in your home, or animals on a farm. The dirt on your (organic) vegetables is beneficial too, so when you prepare them, give them a gentle rinse rather than a scrub. A little dirt goes a long way!

Make your own:

Once you get into the habit of including fermented foods and drinks you’ll start noticing that the price tag, it can add up quickly! It doesn’t have to though, as making your own gives you high quality, health-promoting ferments at a fraction of the price. It might seem intimidating at first, but I promise that it can be easy, and even fun. There’s no better time to start making your own fermented foods and drinks.

About Sarah Ramsden

Sarah Ramsden is a Certified Nutritional Practitioner, teacher and speaker. She’s a brain tumor survivor thriver, and manages multiple sclerosis naturally. Based in Toronto, Canada she works with clients around the country helping them change their expectations and take control of their health. She has helped alleviate everything from autoimmune disorders, to irritable bowel syndrome, adrenal fatigue, mental health issues and blood sugar disregulation. She's the co-creator of S&S TV.


  • Jenny says

    This is the first time I’ve heard that kombucha is better tolerated by those with histamine sensitivity. Do you know why?

    • Sarah of SarahRamsden.com says

      Hey Jenny! Typically fermented foods are high in histamine (no doubt in part because the food sits around for a long time), which is why is problematic for those with the sensitivity. There’s something about the kombucha fermentation process that’s different, and to be honest I’m not certain on the mechanisms behind it, but I have had good results with my clients! Sarah Ballantyne mentioned it in her book “The Paleo Approach” too. If you’re sensitive to histamine, I’d only start with a very small serving to test it out, and increase from there.

  • Claire T says

    Very interesting blog. Have been learning about fermented foods lately. Thankyou.

  • Janette says

    What if you do not like fermented foods except for a dill pickle? Don’t say eat it any way because I can’t. I don’t like the taste. Is their probiotics to take as the next best thing?

    • Sarah of SarahRamsden.com says

      Janette, why not just eat pickles then? There are SO many fermented foods out there, you can keep trying some until you find more that you like.

      • Tracy says

        I have IBD and had J-pouch surgery 20 years ago. I currently have a fistula and would prefer to go the Probiotic path as well. Many foods cause distress to the extent that experimentation is miserable and simply not an option. What would you recommend as a Probitic to start?

        • Mickey Trescott says

          Hi Tracy! I can’t advise on medical conditions since I am not a doctor. You’ll need to ask your doctor if fermented foods are advisable for you or if supplementation with a probiotic supplement is better. Hope it helps!

  • […] guest post A Practical Guide to Fermented Foods for Autoimmune Disease over at Mickey Trescott’s Autoimmune Paleo passes on some tips around the practicalities of […]

  • […] to Last Forever – What A Personalized AIP Looks Like (by Eileen Laird of Phoenix Helix) ♥ A Practical Guide to Fermented Food for Autoimmune Disease (by Sarah Ramsden of SarahRamsden.com) ♥ Living Outside the Beehive (by Sherilyn Shwartz of […]

  • Tomas says

    I have tried probiotics supplement and fermented vegetables and get serious illness
    after about a week.
    I have done some research and it seems like I had die off experiences both times I have tried,
    including vomiting.
    I eat a paleo diet and have cured my acne 95 % but think I need to heal my gut and probiotics is a step on the way.
    For now I´m afraid of starting with probiotics or fermented vegetables again because of how bad I got both times.
    Both times I stopped taking/eating the probiotics because I got so bad.
    Can you please help me with this?


    • Mickey Trescott says

      Hi Tomas!
      I’m so sorry to hear of your issues with taking probiotics and eating fermented foods! Unfortunately there could be a lot of factors to your situation, and you should probably seek the advice of a doctor or a nutritionist to sort out why your reaction was so bad. Sometimes it is something like SIBO, or an intolerance to histamine that can be a problem. Good luck!

  • Ebru says

    I’m doing paleo autoimmune diet since 3 weeks and I’m gonna start eating fermented vegtebales but I have a question. My mom makes some fermented vegtebales at home. For example she makes fermented cabbage. But she puts some chickpeas in it to make it fermented. She cuts the cabbage puts in a big bottle and fill it with water. And she also puts salt and 5-6 chickpeas inside. After one week it’s fermented. And she takes the chickpeas out. What I wonder is that if it’s okay to eat this. Because there is chickpeas inside. I would appreciate if you would help me with this. Thank you so much.

    • Mickey Trescott says

      Hi Ebru!
      Chickpeas are not included on the autoimmune protocol, so if you are going to try a strict elimination you should see if your mom minds trying her recipe without. Chickpeas are not required for fermentation, but I suspect she uses them for flavor. Many of us have made ferments with just cabbage (or other AIP veggies like carrots or beets), water and salt and they come out delicious! Hope it helps 🙂

  • Jeniver says

    Just curious about lacto-fermenting and avoiding dairy. Seems to me to be a little contradictory. Thanks for such a great resource!

  • Sanni says

    Hi and thanks for a great post! I love to use sauerkraut in cooking, but have been wondering how much of the good bacteria get killed when heated?

    • Mickey Trescott says

      Hi Sanni,
      In order to realize the benefits of eating the probiotic food, you’ll want to eat the sauerkraut raw instead of using it for cooking. I’m not sure about the figures on how much bacteria is destroyed.

  • […] the damages caused by autoimmune diseases. Some examples of nutrient-dense foods are bone broth, fermented vegetables, fatty fish, shellfish, and offal. While most of these are already pretty mainstream, some of us […]

  • Carl Maxfield says

    Hi everyone,

    Where can I find the formulas/ best recommendations for food combining autoimmune / paleo?

    • Mickey Trescott says

      Hey Carl! We don’t teach food combining here, if that is what you are asking!

  • Kristine says


    Is the water kefir safe for the AIP diet since it has sugar? Or does enough of it dissolve? I just started making water kefir soda. I have gotten a lot sicker since starting it so I suppose I should back off to 1 tablespoon a day? (I just enjoy the flavor)

    I would like to try the AIP diet

    • Mickey Trescott says

      Hi Kristine! Water kefir is fine on AIP as long as you tolerate it. If you notice symptoms when drinking, it may mean you are sensitive to histamine!

  • Wendy Hui says

    Hi, I have Churg Strauss Syndrome & am currently on Prednisolone & cellcept. Is it all right for me to consume milk kefir? I was advised by my Doctor to advising raw food. Thanks.

    • Mickey Trescott says

      Hey Wendy! Unfortunately, this is a question for you to go over with your doctor, we don’t give medical advice here.

  • Mary says

    Hi guys,
    Do you have any other resources for learning how to properly ferment foods? Sarah’s website seems to be disabled.
    Thank you! 🙂

    • Mickey Trescott says

      Hi Mary! Sorry to hear about Sarah’s site – honestly I would head over to YouTube, there are tons of great fermentation videos there!

  • Shaun V Rickerl says

    I had a question about the fermented vegetables, do you ferment your own and do you have a recipe that you use?

    • Mickey Trescott says

      Hi Shaun! Personally, I don’t make my own ferments very often because I prioritize making most of my own meals from scratch, which is time consuming! I say whether you are making or purchasing, including them in your diet is a great idea – just make sure if you purchase them they are raw and unpasteurized.

  • Brytanny Howard says


    I am new to AIP (About a month in) and I am wanted to try some kombucha drinks again. I am having difficulties knowing which drinks are ok though since all of them include in the ingredients “sugar”.
    Now I don’t know if its sugar added to feed the organism, sugar created as a by-product or simply added to flavor the drink.

    And since sugar is not allowed on AIP I don’t really know where that leaves me.
    Any ideas or info to help me solve my dilemma?

    • Mickey Trescott says

      Hi Brytanny! Great question. So, sugar in kombucha is OK on AIP, but over the years most commercial brands have added more than just to feed the organism, they are also sweetening the beverage. So I’d suggest checking labels carefully and only using brands that are truly low-sugar (if it tastes too good to be true, probably is!). Hope it helps!

      • Maria Aparecida Webber says

        Hello! I really want to try kombucha on my AIP but I’m still free from coffee, green tea and others caffeine ingredients. The kombucha I can find around is always made with green tea plus other ingredientes. Is it ok to drink kombucha from green tea? Is it the same situation as sugar in kombucha? Thank you!!!!

        • Mickey Trescott says

          Hi Maria! Yes, green tea is AIP compliant, and the small amount of sugar used to feed the culture is as well. You do want to check for any other ingredients, and that the brand you pick is not too sweet – there are some that are like soda these days! Good luck!

  • Patty says

    Hi there. I hear so many people talking of he benefits of kimchi (and I have loved it in the past) but I am assuming that is a “no-go” if on AIP because of the red pepper flakes (I have not found a kimchi without)? Do you know if one exists? If my stomach heals well, can someone who has been on AIP consider having again with the red pepper flakes or is it advised one should never have again so as not to cause probs. with leaky gut again?

    Thank you kindly.

    • Mickey Trescott says

      Hi Patty! Yes, you will want to leave out the kimchi on the elimination phase. You can still have ferments without the peppers though – try kraut, fermented carrots, or beets instead! Good luck!

  • Hi thank you for your amazing post. I just started my AIP diet and realized that all fermented vegetables that include probiotics have sugar or ingredients that are not allowed on the AIP such as Sugar, fennel seeds, Vinegar etc. so I am not sure why you mentioned including sauerkraut and kombucha is okay I always thought no sugar is allowed on the AIP?
    I would love to include probiotics into my diet but can’t seem to find AIP-approved ones.

    Thanks so much.

    • Mickey Trescott says

      Hi Kim! There are absolutely AIP-friendly ferments out there. For those veggies, you’ll want to look for products that only contain salt and AIP-friendly herbs. For kombucha, the sugar used to feed the scoby is not eliminated, and you’ll just want to check the other ingredients there. Hope it helps!

  • Barbara says

    Are all SCOBYs aip compliant? Is there a certain one I would want to but if I’m following the aip diet?

    • Mickey Trescott says

      Hi Barbara, I would say generally, yes, but you should inquire with the manufacturer that the only contents are bacteria, yeast, tea, and sugar. Good luck!

Leave a Comment