The Autoimmune Protocol Diet

Medically Reviewed by Jabeen Begum, MD on September 06, 2024
9 min read

The research is clear: No diet can cure arthritis, but can a diet ease arthritis symptoms? Research gives the popular Mediterranean diet high marks for its anti-inflammatory benefits and varied food choices. While vegetarian and vegan diets are more restrictive, studies also show anti-inflammatory benefits.

One more restrictive diet plan you may hear about is the autoimmune protocol (AIP) diet. It’s based on the idea that certain foods inflame your gut and that eliminating them may ease autoimmune symptoms.

It’s important to understand that following the AIP diet long-term can result in nutrient deficiencies that can lead to other complications. Plus, there’s no formal structured plan, so it’s tough to determine if a modified version would be best for your unique needs.

The AIP diet has you focus on eating nutritious whole foods. But at least at the beginning, it asks you to cut out:

  • Grains
  • Legumes
  • Nightshades (potatoes, tomatoes, peppers, eggplant, spices made from peppers)
  • Dairy
  • Eggs
  • Coffee
  • Alcohol
  • Nuts and seeds
  • Processed meats
  • Refined or processed sugars and oils
  • Food additives

That makes it even more restrictive than the Paleo diet, which forbids foods such as grains, dairy, and legumes. Experts also recommend no smoking or using NSAID pain relievers, such as ibuprofen and naproxen.

Once you’ve stopped eating and drinking all of these things, you wait to see if your autoimmune symptoms improve. If they do, you slowly go back to eating the foods you had cut out, one at a time, to find out if any of them trigger your symptoms. The idea is that you’ll learn which foods to stay away from.

This type of eating plan is called an elimination diet. People usually stay on an elimination diet for only about 4-8 weeks.

Following the AIP diet could be risky for your health, so you need to get your doctor’s OK before you try it. If they give you the green light, they have to structure the diet for you and supervise you while you’re on it. It’s also important to let them know if you’re taking any medications or supplements before you start.

Autoimmune diseases -- such as rheumatoid arthritis, psoriatic arthritis, or inflammatory bowel disease -- are long-term conditions where your immune system goes haywire and attacks healthy tissues by mistake. This causes ongoing inflammation in the affected body parts.

Experts don’t know the exact cause of autoimmune diseases. One theory argues that they stem from substances that make their way through your gut lining, get into your bloodstream, and trigger inflammation. It’s called the “leaky gut” theory, and some researchers link it to higher odds of getting certain autoimmune conditions. That doesn’t prove cause and effect though.

The AIP diet aims to support the gut lining and ease autoimmune symptoms by having you avoid foods tied to inflammation. A small study suggested that the diet might improve quality of life in people with inflammatory bowel disease, but the researchers cautioned that larger and more rigorous studies are needed.

More than 100 autoimmune conditions may benefit from the AIP diet. Some of the more common ones include:

  • Rheumatoid arthritis
  • Psoriatic arthritis
  • Multiple sclerosis
  • Sjögren's syndrome
  • Celiac disease
  • Lupus
  • Hashimoto’s disease
  • Polycystic ovary syndrome (PCOS)
  • Adrenal fatigue
  • Ankylosing spondylitis

The autoimmune protocol diet has three phases — the elimination phase, in which you cut out potentially problematic foods; the reintroduction phase, in which you test which of those foods you can safely eat; and the maintenance phase, in which you incorporate what you've learned into a lifelong eating plan.

It's a good idea to keep a food diary during phases one and two where you track everything you eat and any symptoms you have.

Elimination phase

During the elimination phase, you stop eating the potential trigger foods listed above (grains, legumes, dairy, eggs, processed food, nuts, nightshade vegetables, etc.) This may be done all at once, or gradually over a period of several weeks.

Guidance on how long you're supposed to stay in this phase varies, but it's at least a month and up to 3 months. Check in with your doctor or dietitian after about 4-6 weeks to see if your symptoms have improved. If the diet is helping, you should feel better at the end of this phase. If you don't, it may be that what you eat doesn't play a large role in your condition, or that a food that isn't on the general elimination list is a problem for you. Talk to your doctor about other options.

Reintroduction phase

In phase two, you start adding back into your diet the foods you had eliminated. This happens slowly, with one type of food at a time. You and your doctor can decide what order to go in. You may start with a food that has the most nutritional value, or maybe something you've been craving.

Ask your doctor the best way to go about testing each food. One recommended approach:

  • Take a small bite, then wait 15 minutes.
  • If no reaction, take a larger bite, then wait 2-3 hours.
  • If no reaction, eat a regular portion, then stop eating that food for the rest of the week.
  • If no reaction, you can add that food back to your diet.

It can take some time for the food you eat to have an effect on autoimmune symptoms, which is why you need to wait several days to be sure you're in the clear. If at any time during the test period your symptoms get worse, put that food back on the “do not eat” list.

Once you've tested one food, you can move on to another. This phase can go on for months.

Maintenance phase

After you figure out which foods cause problems for you, you can create a long-term eating plan that avoids them. If you find that many foods are problematic, work with your doctor or a dietitian to craft a personalized diet that won't trigger your symptoms but still meets your nutritional needs.

You might choose to indulge in a trigger food every now and then, such as for a special event, as long as the consequences aren't too serious. It's also possible for your body's response to change over time. You can always go back to the reintroduction phase with a particular food, although it's best to wait at least a year.

Every diet has its pros and cons, and some diets are harder than others to stick to. The autoimmune protocol diet is very restrictive at first, but the goal is to identify individual foods that may be contributing to your symptoms and then get back to a more regular eating pattern.

Benefits of the autoimmune protocol diet

If you're able to recognize and cut out problem foods, the AIP diet can help you better manage an autoimmune disease. It can lower the level of inflammation in your body, which plays a role in many health issues. In particular, the diet aims to calm irritation and heal damage in your intestines, which may be linked to autoimmune diseases.

With an emphasis on vegetables, fresh fruits, lean meat, and fish, the AIP diet also gives you lots of important nutrients, including protein, fiber, and vitamins, which benefit your overall health.

Risks of the autoimmune protocol diet

Because you have to cut out so many foods, you could fall short on important nutrients and get other health problems.

Don’t try the AIP diet if you’re:

  • Pregnant
  • Underweight
  • Malnourished

In those situations, if you want to find out whether changing your eating habits might ease your autoimmune condition symptoms, ask your doctor to recommend a less restrictive plan than the AIP diet.

Before you go on a diet that drastically limits what you eat, consider working with a registered dietitian. They can help you plan meals and make sure that you get the nutrition you need by recommending healthy substitutions for the foods you’re avoiding. Don’t start taking any new dietary supplements without talking to your doctor or a dietitian first.

It may seem like the list of foods to avoid on the autoimmune protocol diet is long, but you still have a wide range of tasty, nutritious options.

Vegetables. During the elimination phase, starchy vegetables, legumes, and nightshades are out. That means no corn, beans, peas, tomatoes, white potatoes, or peppers. But you can, and should, load your plate with other veggies, such as:

  • Asparagus
  • Beets
  • Broccoli
  • Carrots
  • Cauliflower
  • Celery
  • Cucumbers
  • Greens
  • Mushrooms
  • Lettuce
  • Onions
  • Spinach
  • Squash
  • Sweet potatoes
  • Zucchini

Fruit. No goji berries — they're a nightshade. Otherwise, fruit is allowed on the AIP diet. But keep in mind that fruit has a lot of sugar, so your doctor may recommend you have it in moderation or only eat it fresh, not dried. Try:

  • Apples
  • Avocado
  • Bananas
  • Berries
  • Cherries
  • Grapes
  • Mangos
  • Melon
  • Oranges
  • Papaya
  • Peaches
  • Pineapple

Lean meat and fish. Avoid anything processed, such as deli meat or hot dogs. For protein, you'll want to choose lean cuts of meat and poultry —the more natural, the better. Think grass-fed beef, lamb, and pork and free-range chicken. The AIP diet also allows all kinds of fish, shellfish, and seafood, preferably wild-caught. Organ meats and bone broth are encouraged.

Healthy fats. Switch out processed vegetable and seed oils for olive, avocado, and coconut oil.

Natural sweeteners. Refined sugar and artificial sweeteners are out, which means most soft drinks, candy, baked goods, and other sweets. But you can satisfy your sweet tooth with natural sweeteners, such as:

  • Agave 
  • Date sugar
  • Honey
  • Maple syrup
  • Molasses

Seasonings. Meals on the autoimmune protocol diet can be full of flavor. Season your food with:

  • Garlic
  • Vinegar
  • Fresh or dried herbs such as basil, cilantro, oregano, mint, and rosemary
  • Spices such as cinnamon, ginger, and turmeric
  • Plain old salt and pepper

 The only seasonings you CAN'T use are those that come from seeds or peppers, including cayenne pepper, chili powder, mustard, nutmeg, and paprika.

Fermented foods. Foods such as kimchi, kombucha, pickles, and sauerkraut are good for your gut health.

With some creative substitutions, you can still enjoy many of your favorite foods. Although you can't have dairy, you can use coconut milk to make a creamy vegetable soup. Arrowroot starch can thicken a sauce. And if you're missing rice or pasta, try riced cauliflower or zucchini noodles.

Here's what a day's eating during the elimination phase of the AIP diet could look like:

Breakfast. A baked sweet potato drizzled with honey, plus a smoothie made from coconut milk, spinach, bananas, and blueberries

Lunch. Grilled free-range chicken on a salad with mixed greens, avocado, cucumber, and mushrooms, tossed with herbed vinegar and extra-virgin olive oil

Snack. Apple slices and peppermint tea 

Dinner. Wild-caught shrimp stir-fried in coconut oil with broccoli, zucchini, cabbage, carrots, basil, ginger, and garlic over cauliflower rice

The autoimmune protocol diet is an eating plan based on the idea that certain foods can cause inflammation in your body that contributes to autoimmune symptoms. You eliminate whole categories of food for several weeks, including grains, beans, dairy, nuts, and processed foods. If your symptoms improve, you add foods back one at a time to test whether they trigger a flare. It can be hard to get all the nutrients you need on an elimination diet like the AIP diet, so talk to your doctor before you try it.

Is the autoimmune protocol diet healthy?

The foods you're allowed to eat on the autoimmune protocol diet are good for you, including fruits and vegetables, lean meat and seafood, and healthy fat. However, you may have a hard time meeting all of your nutritional needs while you're on it. Ask your doctor or a registered dietitian for meal-planning advice.

How fast can I lose weight on the autoimmune protocol diet?

The point of the AIP diet is not to lose weight but to identify foods that may lead to autoimmune symptoms and to allow inflammation in your intestines to heal. However, you may also lose weight because you're limited in what you can eat and you're cutting out things that tend to be high in calories, fat, or both, such as processed food and most sweets.

Is rice OK for the autoimmune protocol diet?

Rice (both white and brown) is a grain and could lead to inflammation and autoimmune symptoms. Avoid it during the elimination phase of the AIP diet.