PSA: Updates to The Autoimmune Protocol

One of the benefits of the Autoimmune Protocol is that it is based in scientific research, but that foundation means that as we learn more about the intersection of nutrition and autoimmune disease, the recommendations that form the basis of the protocol are likely to change.

We’re writing this post today to give you a heads up that there have been some small but important updates to the protocol, especially the reintroduction process (we’ve also made these updates site-wide, so you can find the full updated reintroduction stages in our post Reintroductions on the Paleo AIP: The Definitive Guide and our AIP Quick-Start Guide).

Changes to the foods to include:

Gut-health superfoods: These include high-fiber and phytonutrient fruits and vegetables, cruciferous vegetables, mushrooms, roots, tubers, alliums, extra virgin olive oil, fish, shellfish, honey and bee products, fermented foods, edible insects, tea, and bone broth.

Why this update? Dr. Ballantyne’s research has indicated that the above foods provide extra healing of the gut through various mechanisms, and she decided to give them their own category to give those in the elimination phase some additional encouragement to include them in their dietary template.

In the same vein, we’d encourage you check out Dr. Rob Abbott’s most recent article on the blog, Are You Getting Enough Nutrients on AIP? to learn more about what he is learning about nutrient density and the Autoimmune Protocol during analysis of the AIP Hashimoto’s study that we collaborated on last year.

Changes to the suggested order of reintroductions:

Coffee: Regular coffee consumption has been moved from Stage 3 to Stage 1 (occasional basis) and Stage 2 (daily basis).

Why this update? Although coffee has been shown to be anti-inflammatory for some people and pro-inflammatory in others, it has properties that can improve the gut microbiome composition.

Cocoa: Cocoa has been moved from Stage 2 to Stage 1.

Why this update? Cocoa has an incredibly high polyphenol content, and polyphenols have been shown to have a modulating effect on the microbiome.

Potatoes: These nightshade-family vegetables have been moved from Stage 4 to Stage 3 in peeled form, but remain in Stage 4 unpeeled.

Why this update? White potatoes are an excellent source of resistant starch, which can be supportive of a healthy microbiome.

Cashews and Pistachios: These are not nuts as commonly thought but drupes, and have been moved from Stage 3 to Stage 2 (anyone with an extreme reaction to poison oak or ivy should proceed with caution when reintroducing these foods).

Why this update? Pistachios, specifically, contain fibers that are uniquely beneficial to the microbiome.

Dairy: The most difficult-to-tolerate dairy products (like cheese, cottage cheese, milk, isolates, and ice cream) have been moved from Stage 4 to Stage 3, with a clarification that these products be from grass-fed animals.

Why this update? Grass-fed dairy is a rich source of conjugated linolenic acid, which reduces the risk of chronic disease and inflammation and provides benefits to microbiome composition.

The end goal on the Autoimmune Protocol

These small shifts to the reintroduction stages bring us to an important point about the end goal of a protocol like AIP — to find the least restricted, but most healing diet for each unique individual.

While we do eliminate many inflammatory foods on AIP, some of the eliminated foods are actually nutrient-dense or provide benefits for microbiome health. There is an argument for attempting to include these in the diet, if you find them tolerable.

The comprehensive science of the Autoimmune Protocol can be found in Dr. Sarah Ballantyne’s guide, The Paleo Approach, although these newest updates will not be coming until the second edition which is scheduled to be released in 2021. Until then, we promise to keep you posted on any new research or updates!

About Mickey Trescott

Mickey Trescott is a cook and one of the bloggers behind Autoimmune Wellness. 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 is a certified Nutritional Therapy Practitioner by the Nutritional Therapy Association, and is the author of The Autoimmune Paleo Cookbook, a guide and recipe book for the autoimmune protocol, and AIP Batch Cook, a video-based batch cooking program. You also can find her on Instagram.


  • …and there was much rejoicing. Thank you for the PSA! 🙂

  • Karen says

    Hmm. Probably not the best idea to issue this update on April Fool’s Day. Edible insects, really?

    • Katie says

      Karen, I guess that means you never read Sarah’s book?

    • Mickey Trescott says

      These updates are no joke, Karen!

  • Linda says

    I would like to read more about Dr Ballantyne’s research but can’t seem to find it on hr website. Is it not available to the general public?

    • Angie Alt says

      Linda, her research is readily available in 100’s of articles on her blog + in her books.

  • April says

    A lot of cultures include insects in their diet. Insects are very high in protein, super cheap to raise and process, not to mention plentiful.

    • Angie Alt says

      Yes, April, you’ll find that Dr. Ballantyne is a big supporter of eating insects.

  • Heather says

    Will there be an updated foods to avoid and folds to include list as well as a reintro spreadsheet.

    • Angie Alt says

      We’ve updated our free materials here on the website & in our free Quick Start Guide.

    • Mickey Trescott says

      The foods to avoid and include did not have any major changes so no update there. We did update our reintroduction guide, you can unsubscribe and resubscribe to our email list to get the updated version.

  • Rachael says

    Is this true or a fool?

    • Angie Alt says

      Rachael, it is not an April Fools. We’d never do that to you. 😉

  • Tae says

    Thank you! You guys help keep me on the right track!

  • […] Several foods were recently reclassified in their reintroduction stages. Check it out to see what’s […]

  • […] those following the paleo autoimmune protocol, cacao was recently reclassified as a Stage 1 reintroduction food. This recipe has been edited to reflect the […]

  • Pinkie Pie says

    Seems weird that Sarah Ballantyne would raise chocolate from Stage 2 to Stage 1, since she herself had such a problem with it:

    • Mickey Trescott says

      The AIP is based more on scientific research than personal experience.

Leave a Comment