Autoimmune Nutrition: Top 7 Nutrition Protocols to Consider to Help Calm Autoimmunity

Mar 26, 2021 | autoimmune disease, autoimmune disease prevention

Christina Stapke, RDN, CDCan your nutrition actually influence autoimmune disease? The short answer is, absolutely!

This is exciting because nutrition can be such a valuable tool to have in your arsenal when tackling your autoimmune condition (and really any other chronic health condition, for that matter).

I’m going to discuss several approaches that I and many other integrative and functional medicine providers have used to help individuals to help calm their autoimmune disease. Many of the nutrition protocols discussed are backed by scientific research, while others warrant more. The protocols that could benefit from more research are discussed here because there is compelling evidence through practice that they can get people feeling better.

A quick note on scientific research & nutrition protocols:

Unfortunately, performing “gold-standard” research studies on specific diets and their impact on specific health conditions can be difficult for reasons such as lack of funding in research for nutrition, poor participant compliance in the study and adherence to the diet, and at times the inability to control for other factors (ex: someone following a diet may be more likely to engage in other healthy activities that can influence their autoimmune disease-like exercise, sleep, stress reduction, etc).

Top 7 Approaches to Consider with an Autoimmune Disease:

Now before diving into these, the most important thing to take away from this is that each nutrition protocol must be tailored to what your body needs. One of these protocols that may work great for your friend/family member may not work well for you.

The information discussed below on each nutrition protocol reviews the connections and potential associations to autoimmune disease- not data proving that they are absolutely causing or definitively healing autoimmune disease.

I’ve listed each regimen below from generally least restrictive to most restrictive. Let’s dive in!

1. Gluten Free

Gluten is a protein found in Barley, Rye, Oats(not labeled gluten free) and Wheat (BROW is an easy way to remember this), and it’s restriction has been studied to have a positive impact on autoimmune disease (1). Common foods with gluten are pasta, bread, and many processed/packaged food products.

One connection between gluten and autoimmune disease is increased intestinal permeability or “leaky gut” when eating gluten(2). The idea is that gluten proteins can increase the “leakiness” or permeability of the gut, and as a result food, bacteria, and toxins can get through your gut lining, into your bloodstream and may cause your immune system to go haywire (2).

Think about your intestinal lining like a cheese cloth. Typically, it has very tiny openings for very small food particles to get into your bloodtream. However, when the gut becomes “leaky” from potential triggers such as excessive gluten intake, high stress levels, toxins, too many “bad bugs” in your gut- just to name a few- think of cutting bigger holes in that cheesecloth- more things can get through- even typically “healthy” foods(we’ll talk more on this in the food sensitivity section towards the end).

I typically have my clients remove gluten first if they have an autoimmune disease(or digestive issue for that matter), because it has the potential to support gut restoration and calming the immune system. I also recommend doing specific testing if they would like to know if they are having an immune reaction to gluten. If you currently eat gluten at each meal- you may try starting with cutting it out for 1 week, focusing on things like winter squash, sweet potatoes and fruit as your carbohydrates instead.

2. Dairy (Cow’s milk) Free 

There is some research that correlates cow’s milk intake to the development of Type 1 Diabetes and Multiple Sclerosis(3). One theory on how this might happen, is that the immune system

  • –> Recognizes the cow’s milk protein(s)
  • –> Classifies them as “foreign invaders”
  • –> Produces antibodies to attack these proteins to keep them from harming the body
  • –> Accidentally recognizes other tissues/cells in the body that look like cow’s milk proteins
  • –> Develops antibodies to your own tissue/cells

*I will note that this mechanism is thought to occur with other foods including gluten discussed above.

To clarify, the category of cow’s milk would include any cow’s milk product like cheese as well(I know this can be tough to read for cheese lovers- I was one of them!)- not just milk that you would drink. Since our immune system largely reacts to proteins versus fats some people may be able to tolerate grass-fed butter and especially clarified butter or ghee as these products have very little protein in them.

In practice, I’ve found that SO many people are either allergic, sensitive or intolerant to dairy in some way, shape, or form. At the very least if someone is not willing to give up dairy, I strongly encourage organic, grass fed and fermented whenever possible.

3. Intermittent Fasting & Fasting Mimicking Diet (FMD)

Intermittent fasting has gained a lot of popularity in recent years as a tool for weight loss. While it can be very effective for weight loss and blood sugar issues like prediabetes and diabetes, it can also be an effective tool for managing autoimmune disease (5).

There are several ways to do intermittent fasting, here are some common methods:

  • Not eating for 16 hours overnight and in the morning, then eating during a window of 8 hours daily (6)
  • Not eating/drinking anything but water (and calorie free beverages like coffee/tea) for 24 hours one to two times per week(6)
  • For 3 days in a 7 day cycle, eating a very low amount of calories and protein(5)

Fasting-Mimicking Diet (FMD)

The Fasting-Mimicking Diet(FMD) developed by Dr. Valter Longo typically consists of a 3-5-day long period each month where one consumes a very low amount of calories, where most calories come from healthy fats(ex: avocado and olive oils), and a minimal amount of calories come from protein and carbohydrates. Most protein should come from plant sources, and sea salt can be used for mineral supplementation(20). After this period of 3-5 days, the individual then returns to eating their typical diet.

The FMD is designed for individuals to benefit from fasting while reducing the risks associated with over-restricting calories. The FMD has not only been studied to improve markers for autoimmune disease(5), but also has been shown to improve markers associated with high blood sugar or diabetes/prediabetes(19), support longevity(17), cognitive function(18), and may reduce cancer risk (17).

A benefit of the FMD that I believe makes it more accessible for people is that there are no restrictions on meal timing, and you can technically eat 3 meals a day as long as you are keeping the calories and protein very low(see some sample recipes below). Being able to have this schedule and more guidance around specific meals may also prevent the overeating at afternoon/nighttime meals that I often see when my clients are doing a time-restricted version of intermittent fasting(ex: first meal at 1pm).

Sample meals allowed on the Fasting Mimicking Diet (FMD) (20):

  • Cucumber mint avocado salad
  • Carrot walnut Soup
  • Chilled avocado soup
  • Chia seed pudding
  • Zucchini noodles with vegetables
  • Curried cauliflower soup

There are several mechanisms by which fasting can help calm the immune system down. One of those mechanisms is called autophagy, which you can think of as a “cleaning house” type mechanism where the body clears out debris, damaged cells in the body and increases the body’s ability to clear out toxins and pathogens(7, 8).

This approach is particularly important to talk to your practitioner about as fasting can also be perceived as a stress on the body, and fasting could potentially do more harm than good in some cases(ex: if you have an eating disorder, are adrenally compromised/have “HPA axis dysfunction”, or have thyroid issues). I typically address my client’s stress levels(and potential other “stressors” to the body, like gut infections, toxins, poor sleep, etc) first before recommending consistent fasting.

4. Low Lectin

Lectins are a compound found in highest amounts in legumes like beans, peanuts as well as whole grains (such as gluten) and other nuts. Lectins are thought to be an “anti-nutrient” as they can bind to nutrients such as calcium, iron, zinc, and phosphorus and as a result prevent their absorption(9).

This particular protocol is controversial for recommending it to the general public, because many populations with lower rates of chronic disease have lectin-rich foods like beans and whole grains as staples in their diet. For individuals without digestive disorders, autoimmune disease, or inflammatory conditions like arthritis, I believe lectin-rich foods may be consumed in moderation as part of a balanced, diverse diet (especially if they are prepared in a way that reduces the lectin content like soaking or sprouting).

However, with those dealing with a digestive disorder, autoimmune disease or inflammatory condition, a low-lectin diet may be worth trying. There is some research that points to lectins potentially triggering a similar immune reaction as described with gluten and dairy- the body recognizes the lectin as a foreign invader, then attacks your own tissue that looks similar to it (11).

This is a diet that definitely needs more research in the scientific literature, however in practice it may be a helpful tool in calming symptoms down while we address the root causes of why lectins are triggering your body in the first place.

5. Nightshade Free

Nightshades are a food category consisting of tomatoes, bell peppers, white potatoes, eggplant, and certain spices such as cayenne and paprika that contain compounds called alkaloids(10).

This food restriction to mitigate autoimmune disease is less supported by scientific research, however, anecdotally it has appeared to be an effective method for many individuals especially with conditions like arthritis.

However, the question remains for these individuals who thrive on no nightshades- why can’t they tolerate nightshades when other people can? Not being able to tolerate nightshades ought to be used as a sign to further investigate underlying imbalances in the body.

–> Could it be a gut bacteria issue?

–> Have you developed food sensitivities to these foods? (AND what is causing those?)

–> How much inflammation do you have at baseline?

–> What is triggering this inflammation?

Similar to the lectin-free approach, I encourage you to investigate these questions with your practitioner if you feel a benefit from restricting nightshades in the diet.

6. Autoimmune Protocol (AIP)

The Autoimmune Protocol (AIP) essentially is a combination of all of the above protocols and is the most restrictive. It eliminates (11):

  • Gluten (wheat, barley, rye, oats not labeled gluten-free)
  • Dairy (cow/goat/sheep’s milk, cheese, yogurt, butter)
  • Grains (rice, quinoa, barley, rye, oats)
  • Legumes (lentils, peas, beans, peanuts)
  • Nuts
  • Seeds (particularly cocoa, coffee, spices made from seeds-cumin, coriander, anise, fennel, nutmeg, mustard)
  • Eggs
  • Nightshades (eggplant, tomatoes, potatoes, peppers, paprika)
  • Alcohol
  • Refined/processed sugars and oils(canola, cottonseed, soybean, etc)
  • Food additives & artificial sweeteners

Now I’m sure you’re wondering, what can I eat on this protocol?! (11)

  • Vegetables (excluding nightshades)
  • Fresh fruit in moderation
  • Tubers (yams, sweet potatoes, artichokes)
  • Fresh meat (grass-fed beef, wild game, seafood, pasture-raised chicken)
  • Fermented foods (sauerkraut, kimchi, pickles)
  • High-quality vegetable oils (olive, avocado, coconut oils)
  • Natural sweeteners in moderation (honey, maple syrup)
  • Teas, bone broth, herbs/spices

This protocol involves an elimination phase of 30-90 days, then a reintroduction phase where each food is reintroduced one at a time, separated by 5-7 days to be able to identify any adverse symptoms(11).

The rationale behind removing these foods is to help reduce gut bacteria balance, gut inflammation, and mitigate any possible immune responses to these foods(11).

Needless to say, this can be quite an overwhelming and restrictive protocol, and for a lot of individuals, doing a modified version of this is enough.  But is there research to back this up?

The answer is yes, there is some– but not enough to broadly recommend this approach. There have been some very small studies testing the effectiveness of this diet- a couple of examples look at the effects of this diet on individuals with Inflammatory Bowel Disease (12, 13).

With that said, anecdotally many individuals with autoimmune disease have gotten great results from this approach, and while it’s helpful and important to have more data on this- it’s something that may be worth trying to see if your body responds well to this only with support from a practitioner.

The reason guidance is important especially with this protocol is because it limits a lot of foods. Going on a very restricted protocol like this has the potential to deplete certain vitamins and minerals in your body as well as potentially impact the composition of your gut bacteria, as some of the foods eliminated can serve as food sources for our good gut bacteria (14). A functional medicine practitioner can come up with a plan to support your body best to prevent these kinds of things from happening.

7. Food Sensitivities

Testing for your unique food sensitivities may be the most personalized approach out of all of these protocols discussed, however, there can be limitations to testing. But before diving into this, you may be wondering, what is the difference between food sensitivities, intolerances, and allergies?

They are all unique. This is a good rule of thumb given what we know right now(15):

  • Food intolerance: does not involve immune system
    • Ex: digestive distress after a food
  • Food sensitivity: immune system is involved.
    • Typically involve the IgG and IgA immune cells (or “immunoglobulins”)
    • Ex: headaches, skin reactions, possible digestive issues as well
  • Food allergy: immune system is involved. When severe, it can result in anaphylaxis.
    • Typically involve the IgE immune cells (or immunoglobulin)
    • Ex: hives, rash, throat/tongue swelling

Food sensitivities may tend to fly under the radar as a trigger in your autoimmune condition because testing is not widely used and accepted yet. Sometimes food sensitivities can even have a delayed effect on the body making them difficult to attribute symptoms to. For example, in some cases if you eat a piece of bread today and your body recognizes that as a trigger to your immune system, let’s say you have Hashimoto’s thyroiditis (an autoimmune thyroid condition) and Celiac disease (an autoimmune response to gluten) it may take up to 6 months for your immune system to recover(16).

So how do we develop food sensitivities?

There are a few different ways this can happen, but the most common is via increased intestinal permeability or “leaky gut.” Remember what I discussed earlier with a leaky gut being like a cheesecloth with bigger holes poked in it?

Well, let’s say you have some more permeability or figurative “holes” in your gut allowing for bigger particles of food to get through into your circulation. Our immune systems can recognize these particles as foreign invaders, then mount a full-blown immune response to them. In some cases, these food particles look similar to our own tissues (ex: gliadin, a protein in gluten and thyroid tissue look similar(16)), so our body ends up attacking itself thinking it’s attacking this food “invader.” The thing is, this process can happen with foods not listed throughout this whole post.

When attempting to discover your own food sensitivities, being guided by a practitioner is essential. The practitioner may recommend specific blood testing(ex: peptide(building blocks of protein)-level IgG and IgA testing may be helpful), or possibly a personalized elimination diet for at least 3 weeks to be able to identify what may be triggering your immune system.

Next steps…

Sound like a lot? Remember, you need to understand what exactly is going to be right for you given your history, current symptoms, digestive function, individual food triggers, and so many other factors. Also, most of these diets are intended to be a temporary tool while you work with your practitioner to uncover the underlying causes of your autoimmune disease.

I also want to underscore the importance of checking in on your stress levels and what you have going on in your life when taking on a specific diet (especially a more restrictive one). You can be eating an extremely rigid version of any one of these diets listed above, highly stressed out about it (and potentially isolated from it) and that stress can potentially be sabotaging your progress with the diet.

The best way to go about embarking on one of these protocols is to get personalized recommendations and support from a trained practitioner in integrative & functional medicine and nutrition. Make sure to talk with your functional medicine practitioner about any of these protocols you’d like to experiment with before implementing them!

Christina Stapke, RDN, CD
Virtual Integrative & Functional Nutrition Therapy



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13. Anita Chandrasekaran, MD, MPH, Shauna Groven, BS, James D Lewis, MD, MSCE, Susan S Levy, PhD, Caroline Diamant, MD, Emily Singh, MD, Gauree Gupta Konijeti, MD, MPH, An Autoimmune Protocol Diet Improves Patient-Reported Quality of Life in Inflammatory Bowel Disease, Crohn’s & Colitis 360, Volume 1, Issue 3, October 2019, otz019,

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16. Sategna-Guidetti C, Bruno M, Mazza E, Carlino A, Predebon S, Tagliabue M, Brossa C. Autoimmune thyroid diseases and coeliac disease. Eur J Gastroenterol Hepatol. 1998 Nov;10(11):927-31. doi: 10.1097/00042737-199811000-00005. PMID: 9872614.

17. Brandhorst S, Choi IY, Wei M, Cheng CW, Sedrakyan S, Navarrete G, Dubeau L, Yap LP, Park R, Vinciguerra M, Di Biase S, Mirzaei H, Mirisola MG, Childress P, Ji L, Groshen S, Penna F, Odetti P, Perin L, Conti PS, Ikeno Y, Kennedy BK, Cohen P, Morgan TE, Dorff TB, Longo VD. A Periodic Diet that Mimics Fasting Promotes Multi-System Regeneration, Enhanced Cognitive Performance, and Healthspan. Cell Metab. 2015 Jul 7;22(1):86-99. doi: 10.1016/j.cmet.2015.05.012. Epub 2015 Jun 18. PMID: 26094889; PMCID: PMC4509734.

18. Parrella E, Maxim T, Maialetti F, et al. Protein restriction cycles reduce IGF-1 and phosphorylated Tau, and improve behavioral performance in an Alzheimer’s disease mouse model. Aging Cell. 2013;12(2):257-268. doi:10.1111/acel.12049

19. Malik, R. (2017). Faculty opinions recommendation of Fasting-mimicking Diet Promotes NGN3-DRIVEN β-cell regeneration to Reverse Diabetes. Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature. doi:10.3410/f.727343125.793529502

20. “Homemade Recipes for the Fasting Mimicking Diet”.

“Got a Revolution, got to Revolution.”  Jefferson Airplane


Dr. David Bilstrom
Autoimmune Functional Medicine Doctornatural treatment for autoimmune disease by Dr David Bilstrom Functional Medicine Doctor MD



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