PSA: Further 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 additional small but important updates to the protocol, this time only to 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 suggested order of reintroductions:

Legume Sprouts: Added to Stage 1.

Why this update? Legume sprouts (such as mung bean sprouts) have always been a bit of a gray area, with Dr. Sarah Ballantyne (The Paleo Mom) classifying them similarly to legumes with edible pods. They contain only a fraction of the phytates and agglutinins that dried beans do, and what they do contain is much more easily deactivated by heat. Frequent questions from the AIP community necessitated adding them specifically to the reintroduction stages.

Chia Seeds: Separated from gluten-free grains and pseudograins in Stage 4 and moved to Stage 2.

Why this update? The pseudograins buckwheat, amaranth and quinoa are all rich in problematic compounds, including saponins and amylase-trypsin inhibitors, and the prolamins in both quinoa and amaranth are known gluten cross-reactors. Chia is a different story however, as it comes from a different family than quinoa, buckwheat or amaranth and doesn’t appear to contain the problematic compounds identified in other pseudograins. In fact, the only reason chia hasn’t being incorporated into the elimination phase of the AIP is the lack of information currently available about the impact of its high mucilage fiber content. While mucilage tends to be beneficial for the gut microbiome, it also modulates the immune system in complex and potentially detrimental ways for anyone with autoimmune disease, because there are many unanswered questions about the impact of chia mucilage on immune function, it is initially eliminated on the AIP.

Split Peas, Lentils, and Garbanzo Beans: Separated from traditionally prepared and fermented legumes in Stage 4 and moved to Stage 3.

Why this update? Peas, lentils and garbanzo beans are especially beneficial for the gut microbiome while containing lower amounts of antinutrients and agglutinins that are more easily deactivated by heat than other legumes like kidney beans, soy, and peanuts. For this reason, it seemed prudent to separate them from other legumes and encourage reintroduction earlier than previously.

The end goal on the Autoimmune Protocol

These small shifts to the reintroduction stages bring us again 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 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.


  • Tae says

    Yes! Thank you for your diligence and service to us!

  • LindaR says

    Thank you so much for this information!!!

  • Naomi says

    Thank you for the information! I have just started an AIP program, and I’m always looking for interesting sdditions

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