What is the Autoimmune Paleo Diet?

If you have suffered from an autoimmune disease, want to try to prevent autoimmune issues, or are just looking for a healthy diet that addresses inflammation, the Autoimmune Paleo Diet (AIP) might be what you’re looking for. Currently, autoimmune diseases affect approximately 15% of Americans, and the prevalence of autoimmune disease is on the rise! With diet thought to be a key contributor to these conditions, the Autoimmune Paleo Diet, also called the Autoimmune Protocol, is a dietary approach to battling and preventing chronic disease. So, how does it work?

Paleo Diet for Autoimmune Disease Management

The Autoimmune Paleo Diet is a version of the paleo diets you’ve likely seen before. The difference is that the AIP is focused on providing the body with the correct nutrition for individuals with autoimmune dysfunction. The idea is that by focusing on a diet rich in foods that promote tissue healing, hormone regulation, a healthy immune system, and gut health, people’s bodies can gradually begin to heal. 

Modern food has two components: 1.) Those that support, maintain, and promote health, and 2.) Those that diminish health. While there are certainly neutral components to food, these are not factored in to evaluate food in this diet. For example, foods like seafood, organ meats, and most vegetables contain few to no elements that undermine health but do contain numerous beneficial vitamins, minerals, and other health-promoting factors. It might be obvious that foods like cakes, chips, and candies lack positive qualities, but some of the foods to avoid while on this diet may surprise you!

AIP – What to Eat and What to Avoid

Curious about what to eat and what to avoid while on the Autoimmune Paleo Diet? This list is a great starting point:


  • Trans fats
  • Chemical additives 
  • Artificial colors and flavorings
  • High-fructose corn syrup
  • Grains (particularly wheat, rye, and barley)
  • Pseudograins
  • Legumes (especially peanuts, soy, and kidney beans)
  • Dairy
  • Processed and refined foods
  • Refined sugars
  • Sugar substitutes (this includes Stevia)
  • Refined vegetable oils
  • Eggs
  • Nightshades (including tomatoes, white potatoes, peppers, eggplant, goji berries, and spices sourced from peppers like cayenne and paprika)
  • Alcohol
  • Coffee
  • Nuts
  • Seeds
  • Chlorella and spirulina
  • Dried fruit
  • Chocolate
  • Lectins (found in legumes like beans, lentils, soybeans, peas, and peanuts; grains, and nightshades like eggplants and tomatoes)

See any items on this list that shocked you? You wouldn’t be alone. The AIP diet is known for being restrictive and certainly isn’t for everyone. Nightshades are one of the more controversial categories on this list. Scientists have investigated several compounds found in nightshades like tomatoes that stimulate the immune system so aggressively that they’ve been suggested for use in vaccines to boost immune response!

Similarly, lectins can cause problems within the body. Since lectins are stable in acidic environments, they don’t break down easily in the stomach and can line the digestive tract, preventing the proper absorption of nutrients and upsetting the balance of intestinal flora. Prolonged binding to cells in the digestive system can lead to inflammation and disease. Additionally, lectins are good at crossing the gut barrier, causing conditions like leaky gut that also boost inflammation.

Looks like a healthy plate, right? On the autoimmune paleo diet (AIP), some of these ingredients aren’t allowed!

The good news is that the foods on this list don’t need to be avoided forever. For the most part, the foods with beneficial elements can be reintroduced one-by-one over time. The AIP is best thought of as an elimination diet that floods the body with healing nutrients. By slowly reintroducing the foods that may stimulate the immune system, one can see what foods make them feel worse. Reintroducing foods is often where the diet gets confusing, so it can be helpful to be in touch with a health coach or integrative health practitioner. 

Now that we’ve gone over what not to eat on the AIP diet, what can you eat?


  • Organ Meat
  • Fish
  • Shellfish
  • Leafy vegetables (kale, spinach, lettuce, collards, celery leaves, etc.)
  • Cruciferous vegetables (broccoli, cabbage, kale, turnip greens, arugula, Brussels sprouts, cauliflower, watercress, mustard greens, etc.)
  • Roots, tubers, and squash (parsnip, beets, sweet potato, cassava, carrots, fennel, rutabaga, turnip, acorn squash, spaghetti squash, etc.)
  • Mushrooms
  • Vegetables in the onion family (alliums, onions, leek, garlic, etc.)
  • Sea vegetables (excluding chlorella and spirulina)
  • Healthy fats (olive oil, avocado oil, coconut oil, palm oil, fatty fish, grass-fed animal fats)
  • Probiotic/fermented foods (fermented fruits or vegetables, water kefir, kombucha, coconut milk kefir, supplements)
  • Fruit (limiting fructose intake to roughly 10g to 40g per day)
  • Vinegar
  • Herbal teas
  • Organic/grass-fed animal proteins
When ordering food like fish at a restaurant, pay special attention to whether or not the meal is fried or includes unhealthy dressings.

Keep in mind that if you are allergic or sensitive to any of the foods on this list, you are going to want to cut them out completely. If you are a vegetarian, you may find it necessary to get creative to find meaningful sources of protein in your diet as the AIP diet eliminates many common vegetarian sources of protein.

It’s Not All About Diet

That’s right – the Autoimmune Paleo Diet isn’t all about what you consume! The AIP diet takes a holistic approach to health, suggesting that the whole body and its systems and surroundings should be evaluated. There are many factors that can affect immune function, so it’s crucial to focus on getting enough sleep, managing stress, and maintaining an active lifestyle without overdoing it. These three factors also play a role in gut health and hormone functioning, which impact the immune system. Everything is connected, and although a healthy diet can make an enormous difference, there is no silver bullet when it comes to your health.

To further increase the impact of the AIP diet:

  • Get enough sleep (8 – 10 hours every night)
  • Manage stress through exercise, meditation, and other methods that work for you
  • Nurture your social connections
  • Get outside and enjoy nature
  • Enjoy moderate physical activity
  • Protect your circadian rhythms by being outside during the day, in the dark at night, and by maintaining good sleep hygiene by avoiding blue light at night)

The Autoimmune Paleo Diet is pretty strict. It may not be easy to make so many changes all at once. A holistic health practitioner like Progressive Health & Wellness can help you dive in without getting overwhelmed. If you’d like to learn more about this diet, we’d love to chat with you!

For more healthy tips, join the conversation on our Facebook group, Integrative Health and Nutrition for Chronic Conditions. We post live videos, guides, and other useful information to help you elevate your health and wellness.

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