The Beginner’s Guide to Autoimmune Protocol Diet

The Beginner’s Guide to Autoimmune Protocol Diet

Updated March 28th, 2020

The autoimmune protocol diet (AIP) can be incredibly beneficial for people dealing with autoimmune conditions.

Did you know that autoimmunity is one of the top ten causes of fatality in females under sixty-five years old? According to the National Institutes of Health, autoimmune disorders affect over twenty-three million people in the United States each year. Thankfully, this can be managed with the AIP diet.

Check out our AIP Meal Plans. These plans are a simple, sustainable way to follow the autoimmune protocol diet.

Autoimmune disorders include hundreds of medical conditions that are due to the body’s own immune system attacking its own organs. For example, thyroiditis is an attack on the thyroid gland, Crohn’s disease attacks the gastrointestinal system, multiple sclerosis attacks the nervous system, and lupus primarily attacks the kidneys.

One of the most frustrating things about autoimmune conditions is that there is no curative treatment for them. Current therapies are often aimed at managing the symptoms alone.

By using food as medicine, autoimmune protocol diet (AIP) followers are able to reduce troublesome symptoms and heal underlying imbalances by decreasing inflammation and healing gut dysfunction. The diet focuses on a nutrient-dense intake and eliminates inflammatory and allergenic foods to support the body in cooling down the immune system (which is what’s going awry).

The take home point about the autoimmune protocol diet is that if you have an autoimmune issue, you most likely have a poorly functioning digestive tract. Because your gut is not in the best shape, byproducts of all of the things passing through your intestines are leaking through your gut barrier into your blood stream, causing your immune system to respond. This concept is fundamental to understanding why the AIP works in decreasing inflammation and immune system stimulation.

For more information on Celiac disease, an autoimmune condition, check out: The Ultimate Guide to Celiac Disease


Autoimmune-related diseases occur when your body mistakenly attacks and destroys healthy body tissue. Your immune system creates antibodies to destroy harmful substances known as antigens that find their way into your system.

Some of these antigens include:

  • Unhealthy bacteria
  • Viruses
  • Cancer
  • Various toxins (including environmental ones)

These antigens can be genetically related, a product of your environment, or based on current healthy or unhealthy habits you may have (diet, exercise or lack thereof, alcohol consumption, drug use, smoking, etc.)

When you develop an autoimmune disease, your immune system cannot tell the difference between these antigens and healthy body tissue.

Some autoimmune diseases are:

  • Eczema (as well as various rashes)
  • Chronic fatigue syndrome
  • Asthma
  • Alzheimer’s
  • Graves’ disease
  • Lupus
  • Celiac disease (gluten intolerance)
  • Hashimoto’s thyroiditis
  • Multiple sclerosis
  • Reactive arthritis
  • Rheumatoid arthritis
  • Type I diabetes

As you can see from the list above, autoimmune diseases can affect your blood vessels, connective tissue, thyroid, pancreas, muscles, skin, and red blood cells. They can also affect your mood, energy, digestion, and a whole host of other things.

Some of you may already be experiencing autoimmune-related conditions, while others may now be freaked out and wondering if they have one. For the most part, if you’ve been consuming a mostly processed food diet that consists of industrial seed oils and gluten, there is a good chance that you may have an autoimmune-related condition.

Genetics, heavy metals (mercury), mycotoxins (or molds), infections like candida, chronic inflammation due to food sensitivities (gluten, caffeine, alcohol), frequent consumption of NSAIDs or steroids and alpha-blockers (Advil, etc.), and antibiotics can also contribute to autoimmune-related conditions.

Look for signs such as:

  • Chronic joint pain
  • Rashes
  • Frequent muscle pain and weakness
  • Insomnia
  • Poor cognitive function (foggy brain)
  • Frequent colds/sickness
  • Abdominal pain or constant bloating after eating
  • Blood/mucus in your stool
  • Tingling hands and/or feet


To know for sure whether or not you have an autoimmune-related disease, you can take one of several tests:

  • Antinuclear body test
  • Autoantibody test
  • CBC test
  • C-reactive protein test
  • IgG food test

Because many people with autoimmune-related disease have what is know as “leaky gut”, I’d like to touch on that real quick.

Leaky gut is when bacteria, toxins, waste, or incompletely digested protein and/or fats enter the blood stream because of poor intestinal permeability, causing autoimmune reactions.

80% of the immune system is found in the gut, and much of the focus on avoiding or reducing the effects of autoimmune-related diseases is on healing your digestive system. The GI tract doesn’t just digest and absorb nutrients; it also contains neurotransmitters, hormones, enzymes, and chemical messengers that deliver information to your brain.

For most people, adherence to a strict (and by strict I mean strict) paleo diet for three to four weeks, paired with a more mindful eating approach, will usually alleviate any ailments and help them become healthy again. You can find a list of paleo-approved foods right here to help you get started on this.

But – if you do struggle with an autoimmune condition – the autoimmune protocol diet will be beneficial for you.

What Is The Autoimmune Protocol Diet?


So what CAN you eat? Well, you’re in luck. We’ve put together an awesome graph that shows you the ins & outs of this paleo variation so you can stay on track and stay healthy!

Food Group AVOID EAT
MEATS Factory farmed meats, farm raised seafood Beef, Bison, Chicken, Turkey, Boar, Wild Caught Fish, Game Meats
GRAINS Oats, Rice, Millet, Quinoa (a pseudo grain), Wheat, all Gluten None
LEGUMES All Beans (not including string beans or snap peas), Soy/Edamame and Peanuts Snap Peas, String Beans, Haricot Vert
VEGETABLES Avoid Nightshades, Eggplant, Tomatoes, Onion, White Potatoes, Gogi Berries, and all pepper based spices like cayenne, nutmeg, paprika Everything else! Asparagus, Brussels Sprouts, Cabbage, Leafy Greens, Broccoli Cauliflower, Cucumber, Beets, Squash, Carrots, Sweet Potatoes and many more
FRUIT None All fruits are permitted. *To keep daily fructose intake reasonable try to stick to a max of 2-3 pieces of fruit per day
DAIRY Cheese, Yogurt, Ghee, Butter, Ice Cream, Half and Half Coconut milk (without additives)
EGGS All kinds None
NUTS AND SEEDS Almonds, Cacao, Coffee Cashews, Macadamias, Sunflower Seeds, Pumpkin Seeds, Chia Seeds, Sesame Seeds None
FERMENTED FOODS Fermented Soy products Kombucha, Sauerkraut, Kimchi, Kefir made with water/coconut water
SUGAR AND SUGAR REPLACEMENT All sugars! Sugar, HCFs, coconut sugar, date sugar, corn sugar, stevia, agave, molasses and limit honey and maple syrup None
FATS All Butter & ghee, all Margarines, Canola Oil & all other seed oils Avocado, Avocado Oil, Coconut Oil, Lard, Fat, Olive Oil
FOOD ADDITIVES Carrageenan, Guar Gum, Aspartame, Benzoic acid, MSG, Sulfates/Sulfites, Nitrates/Nitrites None
NSAIDS Ibuprofen, Naprosyn, Naproxen sodium, ketorolac and others None
ALCOHOL Beer, Liquor, even sugar alcohols and extracts (like vanilla extract) None (Sparkling water and Kombucha are great party-substitutes!)

Here’s table in graphic form (you can save it and download it for quick reference).

autoimmune protocol diet food list

How Do I Follow The Autoimmune Protocol Diet?

The autoimmune protocol diet can feel overwhelming at first. Luckily, we hope to arm you with information to make this a little less scary. Follow these tips people to successfully stick to the AIP diet.

Start with basic paleo principles

No gluten, no grains, no legumes, no dairy, no sugar, and no alcohol. You’ve got that down already.

Gluten is inflammatory for the gut and should be removed from the diet of anyone with autoimmune disorders.

Grains and legumes are removed to avoid anti-nutrients like phytic acid and inflammatory lectins.

Sugar and alcohol are removed because they are highly inflammatory and do not bring any nutritional value or healing properties to the table.

If you need a refresher on Paleo, check out our Paleo 101 Starter Guide. 

Avoid nightshade vegetables

Vegetables such as peppers, eggplant, and tomatoes have been found to be particularly inflammatory, causing joint pain, skin irritation, and gut discomfort.

Avoid eggs

Eggs are eliminated because the proteins and enzymes in eggs (and in the white in particular) are able to work their way through the gut lining during the digestion process. Although this can occur in healthy people as well, in those with autoimmune conditions, the egg particulate matter gets through the barrier of the gut lining easily and infiltrates the blood stream, causing immune system stimulation and reactivity.

Avoid all nuts and seeds

Nuts and seeds are high in anti-nutrients such as lectins and phytates. They are one of the most allergenic types of foods and can cause sensitivities in people struggling with autoimmunity. Additionally, the ratio of omega-3 to omega-6 fatty acids is suboptimal in most nuts and seeds. In fact, nuts contain a high amount of omega-6 fatty acids, which are pro-inflammatory.

Keep fruit to a minimum

Try to keep fruit to one to two servings per day. This keeps blood sugar levels stable and also helps you avoid taking in too much fructose, which can be irritating for the gut.

Avoid food additives like guar gum and carrageenan

These additives bring no health benefits and contribute to leaky gut. Other additive like nitrites are inflammatory for the body and can also be allergenic.

Avoid non-steroidal anti-inflammatory medications

Avoiding NSAIDs is about attempting to heal the gut lining, as this is critical in managing autoimmune disorders. This can be tricky because many medical regimens for autoimmune disorders such as rheumatoid arthritis, chronic pain syndromes, and acute bouts of thyroiditis use NSAIDs. Before removing these medications from your regimen, discuss this with your medical provider.

How Long Should I Follow The AIP Diet?

One key to AIP success is to focus on following the diet for a set period of time and to track your symptoms over a number of weeks. How long you choose to stay on the AIP is 100% up to you and should depend on how you feel following the diet.

A strict elimination period of at least thirty to sixty days is recommended, but many people stay on the protocol for months until they start seeing the resolution of their autoimmune symptoms.

By setting a timeline for your elimination diet, you can focus on the healing aspect of the diet and stay motivated with an endpoint in sight.

The 4R Approach

I like the 4R approach for avoiding and improving autoimmune-related diseases.

  • Remove all toxins and gut irritants like alcohol, caffeine, drugs (over the counter, antibiotics, etc.), gluten, dairy, corn, soy, legumes, industrial seed oils, and sugar.
  • Replace with healthy and healing foods like those found on the paleo diet, super foods like bone broth, and fermented foods.
  • Repair with specific supplements such as L-glutamine, zinc, omega-3s, and vitamins A, C, D, and E.
  • Restore with healthy bacteria and probiotics (25-100 billion units), digestive enzymes, hydrochloric acid, and soluble fiber.

How To Reintroduce Foods

While the AIP diet may help you to find out which foods you react to, the strict autoimmune protocol is not necessarily meant to be followed for life.

After removing some or all of these foods for three to four weeks, you can then start to reintroduce them very slowly and one at a time.

On the first day of reintroduction, you may decide to include some dairy, like cheese. After this first day of reintroduction, you’ll want to wait two to three days before reintroducing another food. This is because it can often take 24-72 hours for your body to have a response to what you have eaten.

Aside from some of the more obvious physical reactions, make sure to pay attention to things like your mood, energy, sleeping habits, digestion, headaches and sinuses, bloating, and cognitive function.

It’s a great idea to use a journal throughout this process to record your results, measure progress, and to refer to later on.


The autoimmune protocol diet can be a strict protocol to follow, but the rewards can pay off big time.

Have you tried it before and had success? Let us know your experiences with AIP in the comments.

Check out our AIP Meal Plans. These plans are a simple, sustainable way to follow the autoimmune protocol diet.

Bonus – traveling to another country? We love these gluten-free cards from Legal Nomad that will help you communicate your need for gluten-free foods in different languages. Check them out!

Download Your FREE Paleo Starter Kit Today!

  • 3-Day Paleo Diet Meal Plan
  • Comprehensive Paleo Diet Shopping List
  • 5 of Our Favorite Paleo Diet Recipes

VN:F [1.9.22_1171]

Rating: 5.9/10 (570 votes cast)

The Autoimmune Protocol Diet Guide, 5.9 out of 10 based on 570 ratings

Source Article