The food you eat plays a HUGE role in the development of chronic illness. Lifestyle changes like following an AIP diet can be used to halt or reverse disease progression. Food is your primary source of the nutrients needed to achieve optimal health. Unfortunately, nutrient deficiencies are one of the main underlying causes of autoimmune disease and its progression. If you are on the autoimmune spectrum, you’re more likely to be deficient in nutrients such as vitamin D and B12, both of which are crucial for immune function. With the use of these foods in your autoimmune diet, you can find relief from conditions including lupus, rheumatoid arthritis, and Hashimoto’s.

In working with thousands of autoimmune patients, I found that ensuring optimal nutrition is the #1 way to reverse chronic conditions and get relief. In this article, I’ll cover how to prevent nutrient deficiencies linked to autoimmune disease with the best food sources of essential vitamins and minerals to add to your AIP diet. Eating these foods as part of your AIP diet can improve your overall health and give you more energy. Including them may even help you feel better in your body every day.

Why an AIP Diet?

The autoimmune protocol, sometimes called an autoimmune diet or AIP diet, is designed to help reduce the pain and inflammation that comes with being on the autoimmune spectrum. If many of your symptoms seem to mysteriously come and go, such as brain fog, fatigue, headaches, joint pain, or digestive issues, an AIP diet might be right for you. The autoimmune diet eliminates toxic and inflammatory foods and replaces them with foods rich in essential vitamins and minerals. Following an AIP diet can help heal your gut, reduce inflammation, and move you back down the autoimmune spectrum. 

Our AIP Food List

Listed below are my top 6 best food sources for key nutrients on an autoimmune diet. 

6 Best Foods for an Autoimmune or AIP Diet – Featured Image – Amy Myers MD®6 Best Foods for an Autoimmune or AIP Diet - Featured Image - Amy Myers MD® Best Foods for an Autoimmune or AIP Diet – Featured Image – Amy Myers MD®

1. Grass-fed Lamb

Getting enough high-quality animal protein as part of your AIP diet is essential to build and repair tissues, make hormones, and support healthy muscles, cartilage, skin, and blood.1 It’s why I recommend an AIP diet with plenty of meat to anyone with an autoimmune or thyroid condition. Animal protein contains the essential amino acids that are the building blocks for immune function and thyroid hormones. Unfortunately, these amino acids can be difficult to get from other sources, even foods within the autoimmune diet.

Grass-fed lamb is a fantastic source of protein while doing an elimination or AIP diet. It also contains the most vitamin D of all meat—61 micrograms per kilo, which is three to six times the current recommended daily allowance (RDA).2

Vitamin D stimulates your T cells and teaches your immune system not to attack your body’s own cells. The “sunshine vitamin” also helps fight off viral and bacterial infections, which can trigger or make autoimmune conditions worse.

Medical experts dispute how much vitamin D you need each day to maintain optimal health. Studies show that 25-100 micrograms or 1000-4000 IU is required per day. However, the RDA is a mere 10-20 micrograms, or 400-800 IU daily.

I recommend grass-fed and organic meat to patients both on and off an AIP diet because conventionally raised animals are fed an unnatural diet of GMO corn and soy.

Lamb as part of an AIP diet is also a good source of the following essential nutrients:

  • Iron
  • Amino acids (such as L-Tyrosine and L-Glutamine)
  • Choline
  • COQ10
  • Collagen/gelatin
  • Conjugated Linoleic Acid (CLA)
  • Alpha Linoleic Acid (ALA)

2. Wild-caught Fatty Fish

Fatty fish are a major source of the Omega-3s you’ll need while following an AIP diet. Omega-3s enhance B-cell activation and antibody production, which can reduce inflammatory responses and help your immune system fight off pathogens.3

The Omega-3 content of fish varies widely. Cold-water fatty fish such as salmon, mackerel, tuna, herring, and sardines contain high levels of Omega-3s. Fish such as tilapia, cod, and bass, as well as shellfish, contain less.4

To get the daily recommendation of Omega-3 fatty acids while following an AIP diet, you would only need to eat about 5 ounces of salmon, yet 2 pounds of lobster!

Wild-caught fish and farmed fish also have different properties to consider when choosing the best food source of Omega-3s for a nutrient-dense AIP diet. The quality of farmed fish depends on the type of fish pellets they use. Farmers often feed young salmon pellets made from plant and animal sources. Then they add more fish-oil-enriched pellets later in life to fatten them up. This means they spend more time eating a lower quality diet and provide you with fewer nutrients. Wild-caught salmon eat a natural, healthy diet of insects, plankton, and other fish their entire lives. This keeps them lean and packed with antioxidants, including free-radical scavenging astaxanthin.5

Not only can you see the effects of this natural diet in the brilliant red color of wild-caught salmon, you can taste it, too!

3. Avocados

Avocados are an incredibly nutritious and delicious choice for your AIP diet. They’re full of good fat, fiber, vitamin E, copper, and potassium. Furthermore, they are beneficial for your immune system because they are so high in B vitamins.  An AIP diet rich in a variety of B-vitamins is helpful for an overall boost in immune function.6

One-third of a medium avocado as part of an AIP diet provides a wide range of B-vitamins, including:

  • 4% of the RDA of thiamin (B1)
  • 8% of the RDA of riboflavin (B2)
  • 6% of the RDA of niacin (B3)
  • 15% of the RDA of pantothenic acid (B5)
  • 6% of the RDA of pyridoxine (B6)
  • 10% of the RDA of folate7

I often carry an avocado in my purse when I travel. That way I can enjoy a tasty AIP diet-friendly snack that comes in its own handy package!

4. Garlic

Another food I recommend you add to your AIP diet is garlic. Garlic is a prebiotic, so it feeds good bacteria in your gut. This can be helpful if you’re suffering from an autoimmune disease because your gut and your immune system link together.8,9

Friendly gut bacteria bolsters your immune system, and keeps bad bacteria and yeast in check: an AIP diet plus!

Garlic also contains selenium, which helps regulate excessive immune responses and chronic inflammation in people with autoimmune diseases.10

Additionally, selenium is a vital mineral for supporting your thyroid. Studies have shown that people with Hashimoto’s who increase their selenium intake can decrease thyroid antibodies by almost 64%!11

To ensure optimal selenium levels, add garlic, grass-fed beef and poultry, and fatty fish such as salmon to your autoimmune diet.12

5. Grass-fed Beef

One of the most important nutrients to include in your AIP diet is zinc. Zinc supports your immune system in many ways, including regulating your lymphocytes (a type of white blood cell) and protecting you against pathogens.

While following The Myers Way® or doing an AIP diet, zinc can be hard to come by, especially if you are not already taking a daily multivitamin. That’s because zinc is primarily found in foods such as whole grains, legumes, nuts, and seeds—all of which can cause immune flare-ups. One of the best AIP diet, autoimmune-friendly sources of zinc is grass-fed beef. A single serving of beef contains roughly half of your daily requirements for zinc.

I recommend organic, grass-fed beef over conventionally raised meat while following an AIP diet. Conventional livestock is exposed to GMOs, added hormones, and antibiotics. Plus, studies show that animals raised on a healthy, natural diet of fresh grass are higher in vital nutrients, including anti-inflammatory Omega-3s I mentioned were essential while on an AIP diet.13

However, grass-fed beef can be hard to find. That’s why I rely on Butcher Box to deliver 100% grass-fed, grass-finished beef directly to my door. 

6. Leafy Greens

Eating plenty of greens is a key part of an autoimmune diet. Leafy greens are rich in magnesium, which is important for healthy immune function. The average American diet contains barely 50% of the conservative RDA for magnesium. It’s estimated that around three-quarters of the population may be deficient.14

Magnesium deficiency has been shown to increase the production of pro-inflammatory cytokines, which raise inflammation levels, therefore contributing to autoimmunity.15

The current RDA for magnesium is 420mg.16

Just 1 cup of cooked spinach provides 157 mg or 39% of the RDA. It’s fairly easy to get enough if you make leafy greens part of your everyday or AIP diet. Other sources of magnesium include Swiss chard and kale, providing 36% and 18% of your RDA respectively. My nutritional powerhouse Organic Greens Powder is a surefire way to get all the benefits greens have to offer including magnesium, B vitamins, and other essential nutrients. The convenient powder is also delicious in a smoothie or even a glass of water! Plus, it’s a cost-effective way to obtain these nutrients from all organic produce, without any GMOs that can exacerbate autoimmunity.

Optimal Diet & Nutrition for Autoimmune Disease

I have seen it time and time again after working with autoimmune patients from all over the world—eating an AIP diet full of foods rich in essential vitamins and minerals is the first step to reversing your condition. You need them for optimal immune function! My bestselling book The Autoimmune Solution Cookbook is an excellent resource for learning how to create AIP, autoimmune-friendly meals, and AIP snacks. It even uses the 6 foods featured in this article! You will find that The Autoimmune Solution Cookbook is so much more than just a cookbook—it is a roadmap for preventing and overcoming autoimmune diseases. I offer you step-by-step guidance to make The Myers Way® a way of life with mouth-watering, AIP diet-approved plates worth showing off!

What’s more, I have a ton of AIP-friendly recipes on my blog that are FREE for you to enjoy.

Achieving optimal nutrition is key to preventing and reversing autoimmunity and other chronic conditions. Let’s face it though—even the healthiest eaters sometimes have less than optimal levels of essential vitamins and minerals. This could be for various reasons, including:

  • Sometimes you just don’t have the time to cook up complete meals to fit your AIP diet.
  • Our food isn’t what it used to be nutritionally thanks to soil depletion and environmental toxins.
  • You may be struggling with leaky gut, small intestinal bacterial overgrowth (SIBO), or other disorders that keep you from absorbing all the nutrients you get from a good AIP diet.

You don’t want to just want to meet the minimum RDA needed to prevent deficiency-related issues, you want to exceed it! That’s where supplements come in!

Enrich Your AIP Diet with The Best Supplements!

My top four Bestsellers provide you with all of the protein, amino acids, B vitamins, and micronutrients you need to thrive while on an AIP diet!

  • Collagen Protein: packed with amino acids to help maintain and promote optimal gut health
  • Organic Greens: provides all the benefits of leafy greens, including B vitamins, magnesium, phytonutrients, and antioxidants in a convenient powder form
  • The Myers Way® Multivitamin: provides optimal levels of selenium, zinc, iodine, and other essential nutrients to support thyroid health, immune function, and general wellness
  • Paleo Protein (all flavors): contains 21g of protein to build and repair tissues, make hormones, and support healthy muscles, cartilage, skin, and blood

I personally swear by these products and use them every single day!

Paleo Protein Vanilla container


What foods should I avoid on the AIP diet?

The most toxic foods to stay away from while following an autoimmune diet are sugar, alcohol, caffeine, GMO’s, artificial sweeteners, additives, preservatives and dyes, high fructose corn syrup, trans or hydrogenated fats, and all processed, junk, and fast foods that are packed with chemicals and added sugars.

How long should I follow the AIP diet?

I recommend that you remove toxic foods from your diet permanently. After at least 30 days on the autoimmune diet, you can begin to slowly introduce inflammatory foods such as corn, soy, eggs, citrus, or legumes one at a time in order to test your body’s response to individual foods.

Can I follow other diets while on the AIP diet?

Yes! With just a few easy swaps, you can enjoy the full benefits of diets such as Paleo and keto while on an autoimmune diet.

Article Sources

  1. Benefits of Protein. Nourish.
  2. Natural Vitamin D Content in Animal Products. Alexandra Schmid, Barbara Walther. NCBI. 2013.
  3. DHA-Enriched Fish Oil Targets B Cell Lipic Microdomains and Enhanced Ex Vivo and In Vivo B Cell Function. Eric A Gurzell, Heather Teague, Mitchel Harris, Jonathan Clinthorne, Saame Raza Sheikh, Jenifer Fenton. Journal of Leukocyte Biology. 2013.
  4. Omega-3 Fatty Acids. National Institutes of Health. 2021.
  5. Pacific Salmon. Ryan Hagerty. Defenders of Wildlife.
  6. Vitamins: Key Role Players in Boosting Up Immune Response - A Mini Review. Muhammad Farhan Aslam, Sidra Aslam, Jazib Ali Irfan. Vitamins & Minerals . 2017.
  7. Avocado Facts. California Avocado.
  8. Study on Prebiotic Effectiveness of Neutral Garlic Fructan In Vitro. Ning Zhang, Xuesong Huang, Yanhua Zeng, Xiyang Wu, Xichun Peng. ScienceDirect. 2013.
  9. Gut Microbe Drives Autoimmunity. Harrison Wein. NIH. 2018.
  10. The Role of Selenium in Inflammation and Immunity: From Molecular Mechanisms to Therapeutic Opportunities . Zhi Huang, Aaron H Rose, Peter R Hoffman. NCBI. 2012.
  11. Selenium Supplementation in Patients with Autoimmune Thyroiditis Decreases Thyroid Peroxidase Antibodies Concentrations . Roland Gartner, Barbara C H Gasnier, Johannes W Dietrich, Bjarne Krebs, Matthias W A Angstwurm. JCEM. 2002.
  12. Selenium in Garlic. Michelle Kerns. Healthy Eating.
  13. Conjugated Linoleic Acid Content of Milk From Cows Fed Different Diets. T R Dhiman, G R Anand, L D Satter, M W Pariza. NCBI. 1999.
  14. Dietary Reference Intakes for Calcium, Phosphorus, Magnesium, Vitamin D, and Fluoride. National Academic Press. 1997.
  15. Cytokines in Autoimmunity: Role in Induction, Regulation, and Treatment . Kamal D Moudgil, Divaker Choubey. NCBI. 2011.
  16. Top 10 Foods Highest in Magnesium. Daisy Whitbread. MyFoodData. 2021.