Personalized AIP

The Autoimmune Protocol (AIP) was first floated as a dietary concept in about 2002, when Dr. Loren Cordain began theorizing that adjustments to a Paleo diet could support healing in those with autoimmune disease. AIP in it’s more recognizable form has been around since about late 2011, when Dr. Sarah Ballantyne started her blog, The Paleo Mom, and started refining the AIP concept.

The Autoimmune Protocol now is known as a science-based elimination and reintroduction diet and lifestyle protocol, focused on repairing gut health, balancing hormones, and regulating the immune system. The dietary component includes removing food-driven sources of inflammation and restoring nutrient density, while the lifestyle component includes approaches to sleep, stress management, movement, and connection (both with humans and nature), in order to help best manage autoimmune disease. Tens of thousands (if not millions) of people have used it successfully alone or in combination with conventional treatments, depending on their needs. Here at Autoimmune Wellness, we have taken the template Dr. Ballantyne refined after combing through the existing literature and made sure it was then thoroughly studied in actual human beings, so AIP has even been the focus of medical research.

In all that time, despite lots of effort to clearly communicate it by all the leaders in the AIP community, one very persistent misunderstanding has hung around . . . the idea that AIP lasts forever.

The Goal

With AIP, the goal is to eventually arrive at the least restrictive diet that supports the most health and wellness for you as an individual. There are no gold stars for the longest, most perfect AIP elimination phase. Instead, you begin with the end in mind; “What is the least-restrictive diet that still makes me feel great?”

In case you’re missing it here, what you are working toward is personalization. Your end result will look different from any other person using the protocol. You can use the elimination and reintroduction process to your advantage, identifying which foods are causing symptoms, expanding your diet to include foods that are more supportive, and eliminating long-term the foods that you continually find are not a good match for maintaining your health.

The Big Misconception

Notice that important word I used in describing the goal of AIP: reintroduction. The big, persistent misconception with AIP is that it is solely an elimination diet and after we’ve diligently eliminated a long list of foods, we just stay there for the rest of our lives. But that’s not true!

The dietary component of AIP is basically a two phase process, implemented over three stages. The two phases are: Elimination and Reintroduction, which are achieved in three stages: Transition, Maintenance, and Reintroduction.

The Transition and Maintenance stages together constitute the first phase of AIP known as “elimination.” The Reintroduction stage constitutes the second phase of AIP where the focus is no longer on eliminating, but instead on bringing certain foods back into the diet.

Stage 1: Transition to Autoimmune Diet (Elimination Phase)

Transition is the process of moving your diet to the elimination phase, with a focus on nutrient-density. This can be a slow-and-steady process or a cold-turkey process. Most folks are best suited to a slow-and-steady transition.

Stage 2: Maintenance (Elimination Phase)

Maintenance is the period following full transition. The focus is to maintain the food eliminations while concentrating on nutrient-dense additions, with a goal to maximize healing. Maintenance needs to be 30 days at a minimum for everyone, as this cleans the slate for a clear reintroduction process. For most, 60-90 days in Maintenance is more ideal and allows the most healing.

If by 90 days progress is not as expected, it is time to enlist the help of doctors or allied healthcare providers to dig deeper into possible obstacles that cannot be addressed through dietary changes alone and are preventing progress with AIP.

Stage 3: Reintroduction (Reintroduction Phase)

Reintroduction is the second phase and final stage in the process. This stage is reached when a person has spent 30-90 days fully compliant in the elimination phase and has had measurable improvements in their symptoms from their baseline as evidenced from tracking and journaling (and/or lab testing). Ideally, there will be relief of symptoms.

During the reintroduction phase, you progress through a process of testing your response to the foods you’ve eliminated one-at-a-time. At the end of this stage your diet is individualized, sustainable (both practically and socially), and nutrient-dense. Again, it should be the least-restrictive diet that gives you the best health.

But Why?

I think there may be a few reasons this big misconception has persisted so long.

Reason #1: False impressions. One of them is that a lot of the leaders in the AIP community, Autoimmune Wellness included, focus our blogs on navigating the elimination phase of the AIP. Everyone knows that elimination tends to be the biggest challenge, especially when a person first transitions. It’s helpful to have a lot of guidance and support for this part of the journey. The downside to that is that it gives the impression to LOTS of people (combined our websites, podcasts, books, and social media are reaching millions and millions of people) that the elimination phase is forever and that all of the leaders are still strictly in the elimination phase themselves.

Reason #2: The Telephone Game. I think this incorrect impression is then amplified further in some of the very large AIP support groups that exist on social media and are led by individuals who want to help others, but don’t have any professional experience or training in nutrition or health coaching. It’s kind of a “telephone game” effect and misinformation can easily spread in these settings and sometimes group administrators become dogmatic about the strictness required for any healing dietary template. Don’t get me wrong, finding support among our autoimmune peers is crucial! We just have to practice awareness about the kind of community care we are getting.

Reason #3: But why? My professional experience working with thousands of people through my AIP group health coaching programs tells me that the last reason is the really important one behind this persisting misconception that strict AIP has to last forever. If you feel good after eliminating all those foods, why bring them back into your diet? Especially when people finally feel good, I notice that some food fears can develop around advancing to the reintroduction process.

However, reintroduction is important for many reasons:

  • Some of the elimination foods are valuable to re-incorporate into your regular diet from a nutrient standpoint (eggs, for example).
  • Both from a practical and social sustainability standpoint, reintroductions are a wise step (i.e. it’s easier to travel if you can eat rice and it’s nice to occasionally go out to Happy Hour with friends).
  • Finally, there is psychological benefit in working towards expanding your diet as your wellness returns, rather than allowing food-driven fears to take hold. This helps us avoid leaning into disordered eating territory.

So, How Do You Personalize AIP?

Okay, so now you know:

  • what AIP is and where it came from,
  • what the actual goal of AIP is,
  • what the biggest misconception about AIP is,
  • where that misconception originates,
  • and, why reintroductions are so important.

Let’s talk about what you can do to successfully personalize AIP for yourself.

Do a good job with your elimination phase. Ideally, you want to maintain the full elimination phase for at least 30 days. This helps you clear the slate and will make the process of identifying foods that do or do not work for you during reintroduction much, much more clear. This means doing your best to achieve 100% compliance in this period. Following through for 30 days is pretty achievable, but it gets a lot more challenging if, as is very often the case, we need 60-90 days to see measurable results.

The best way to make the elimination phase sustainable is to give yourself time transitioning to it, making sure you develop a strong foundation. A strong foundation means determining a meaningful “why” for yourself, having a good support system, implementing a really strong weekly planning and prep rhythm around food, being mindful of adding in nutrient density, and taking time on the lifestyle piece of the protocol (it’s amazing how much better we can stick to a new dietary change if we’ve had a good night’s sleep!).

One reason for taking your time developing this strong foundation is because it means you won’t have to rely on willpower alone during the elimination process. Willpower is a finite resource, so getting good habits and support in place means you won’t use up so much of it. The other reason for taking your time on foundation building is that it allows you a period of working on progress over paralyzing perfectionism.

Follow the reintroduction process methodically. The reintroduction process can be tricky to implement, because it requires a lot of patience and focus. The most common mistake is rushing the reintroductions and totally confusing the results. After all your effort in the elimination phase, you want to take time for careful communication with your body during reintroductions so you can gain the most information about what foods work for you vs. what foods don’t. To learn more about the reintroduction process, read our Definitive Guide to Reintroductions.

Carefully track to help yourself determine thresholds. As you go through the reintro process you’ll find that some foods immediately cause symptoms and are clearly not a match for you. Others might only be mildly inflammatory for you though and you’ll see that eating them occasionally is fine, but you won’t necessarily want to incorporate them daily. Diligent tracking during the reintroduction process will help you notice these differences and allow you to make really informed decisions about how you want to eat to support your health long-term.

Don’t give up. If at first you aren’t able to reintroduce many foods at first, don’t throw in the towel or worse yet, restrict further. You may just require more healing time. Also notice that just because one food wasn’t a match for your body, doesn’t mean they will all be in this category.

Enjoy your healing. It’s easy after a long period of being very ill or in realizing that the chronic nature of autoimmune disease means a lifetime of managing it, to become a “health miser.” It’s like, “Now that I’m feeling better, I’m going to hoard this health.” And if a reintroduction doesn’t go well, we can be tempted to get even more tight and closed up. Instead, try to focus not on what has gone wrong, but on all the healing you’ve already achieved. Celebrate the foods that are working well for your body, instead of fixating on those that aren’t working. Beginning the process of personalizing your diet is a milestone in expanding your life, not contracting it.


Personalizing your dietary template will take time and persistence. It won’t happen in a few weeks or even months. I’ve been in this process for years and I continue to troubleshoot and edit, as my life and health needs change. That’s what’s so great about a template though, as you learn more about your body through the personalization process, you can adjust your diet based on the ebb and flow of your daily life. It’s a little like sailing. In times of high stress or flare, you “batten down the hatches.” You can tighten your approach to the diet and lifestyle that you know is most suited to you and help restore balance. In times of low stress or really good health, you can “unfurl the sails,” embracing a more expansive approach that allows you to enjoy life and experience your fullest wellness, despite autoimmune disease.

Now share with us! We genuinely want to know what our community has experienced in learning about AIP and yourselves. Did you initially fall into the misconception that you had to do strict elimination phase AIP forever? How did you realize that wasn’t the goal and what has it looked like for you for personalize AIP?

About Angie Alt

Angie Alt is a co-founder here at Autoimmune Wellness. She helps others take charge of their health the same way she took charge of her own after suffering with celiac disease, endometriosis, and lichen sclerosis; one nutritious step at a time. Her special focus is on mixing “data with soul” by looking at the honest heart of the autoimmune journey (which sometimes includes curse words). She is a Certified Health Coach through the Institute for Integrative Nutrition, Nutritional Therapy Consultant through The Nutritional Therapy Association and author of The Alternative Autoimmune Cookbook: Eating for All Phases of the Paleo Autoimmune Protocol and The Autoimmune Wellness Handbook. You can also find her on Instagram.


  • Elly says

    I was diagnosed in March, 2021 with Hashimoto’s. After the diagnosis it was easy to see, hindsight, the changes in my body. First, my nails became brittle and soft like paper. Throughout my life I have always had strong fingernails and hair. They both grew very fast and my hair never split and was very healthy. I thought it was new nail polish causing my nail issues, but it wasn’t. Then I had very painful swelling to my inner elbow (worse on L which is my dominant hand) and bilateral bicep/tricep swelling. They were so bad that all I could do was lay in bed. I already have other co-morbidities (endometriosis, asthma). My last surgery was in 2016 and I have never fully recovered. I was left with bilateral meralgia perestetica and taking pain medications throughout the day. That hasn’t changed but at least with the AIP the swelling in my arms decreased by about 60%. I still have it. I hope it gets better. I am still on the AIP but I successfully reintroduced coffee and dairy but had a severe reaction to tomatoes when I tried. It took 3 weeks to get over it and I am hesitant to try anything else right now. I have been in pain x 6 years, quite significant as well. I need nerve blocks in both sides of my pelvis to help manage my leg pain. I use cognitive behaviour therapy to help me get through my days.

    • Angie Alt says

      Elly, I’m so sorry to read about your long journey w/ chronic pain. I have endometriosis too and can understand. I’m glad to hear that AIP has helped you better manage some aspects of your health, thanks for sharing.

  • Christine Clark says

    I am a few years into my own personalized version of AIP, and your summary of the path mirrored my experience. Thanks so much for your informative articles. Your website and cookbooks made the elimination phase so much easier; I have shared your website with many friends and acquaintances in the last few years. Your cookbooks are still well-used in my house because your recipes are so very simple and tasty. Thank you for providing this lifeline of support for so many!

    • Angie Alt says

      Thanks for sharing your path, Christine, & we are so glad our resources made such a meaningful difference on your journey.

  • Loretta Peeples says

    I truly enjoy the recipes that you give in your e-mails. AIP has been a long journey for me, which started in 2018. At first, I just had digestive problems and my GI doctor said, “No dairy”. I managed that, but still had problems. Next, I found out I have Hashimoto’s, and I eliminated gluten. Next, I was diagnosed with Sjogren’s autoimmune disease! No more nightshades. Then it was a non-alcoholic fatty liver disease! Trying to lose weight, although I’m not really obese, I’ve given up 99% of sugar and starches. Still not losing weight! I’ve never been into cakes or pies or ice cream or sodas, so that part was easy for me.
    When reading your e-mails, gives me courage and a positive outlook. I’m looking forward to reintroducing the foods that I love but have given up. Thank you for all your encouragement.

  • Laurie Wardle says

    I think personalizing AIP is it’s own journey. I stayed in the elimination phase for two years. It wasn’t due to food fears or a misunderstanding of the process. Simply put, I wasn’t emotionally ready to move out of the phase. I had been sick for so long and recovery in the elimination phase was not instantaneous. It took awhile to get my numbers down, to gain endurance (I was just so tired all of the time.), and to recognize stress and how to manage it. When I was ready, I moved on and now have been in a personalized program for almost a year. I love your gentle start program (6 weeks). I approached the introduction phase in much the same manner giving myself permission to take the time needed.

  • Carol says

    How do we find this article or others to refer back to? I don’t see a link on the website.

    • Mickey Trescott says

      Hi Carol! Which article are you referring to? You can save the link at the very top of your browser page.

  • Maggie says

    I’ve been alternating between elimination and reintroduction for a number of years by doing a 40-day elimination during Lent (I recognize that it’s not exactly in the spirit of Lent but for some reason it’s easier to do during that time) and methodical reintroductions starting with foods I can tolerate afterwards. I’ve found this really helps me focus on my health and how my body/brain feel (I have RA) as well as my awareness of what foods are just fine for me and that some foods that used to be well-tolerated are now better left off the menu. As I said before, this has worked well for me – I feel really good and haven’t had to use any biologics! – but if there’s a better way to do this once a year “reset”, I’m happy to do it.

    • Mickey Trescott says

      Maggie, I think it is a really creative approach to try elimination during Lent! Great work and wishing you well!

  • Mariëlle says

    Good article

    How to find out if there are allowed foods which aren’t good for you…that’s also a possibility I gues….

    • Mickey Trescott says

      Hi Marielle! That is always a possibility, but as you develop the skill of learning to feel the experience of different foods might lead you to some new insights.

  • Birgitte Kjøller Pedersen says

    I am in your target group here.

    Thank you for your work, inspiration – and good advice.

    I have lived in the elimination phase practically since October and am hesitant to move on.
    I reintroduced pepper and egg yolk and whites (my husband is the cook and he longed for it), almonds and potatoes (which I LOVE). But during Christmas my system went out of sync. I cheated, not very much, but I indulged.

    I started January on the elimination phase and have stayed there.

    I am focused on my stools and register every detail. They change, the little rats – though my diet is not. I have realized, that that is probably the wrong way to go about it, but I have never had physical pain or other obvious signs to go by.

    My doctor refuses to give me a test for the hashimotos antibodies, I aim at eliminating, and the private lab has not returned results. So I feel at a loss.

    I have come to believe that constipation and itching are long-term consequences, but am I wrong? Shall I give up monitoring my stools as a baseline?

Leave a Comment