Autoimmune Protocol Diet: A Beginner's Guide

The autoimmune diet, a severely restrictive elimination diet, is designed to help you better understand your trigger foods and reduce symptoms.

Chelsea Rae Bourgeois, MS, RD
— Signos
Health writer
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Updated by

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Science-based and reviewed

February 29, 2024
January 8, 2024
— Updated:

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Autoimmune diseases, such as celiac disease, inflammatory bowel disease (IBD), and rheumatoid arthritis, can be at the root of many unwanted and debilitating symptoms.1 Inflammation and pain can take a toll on your immune system and affect your quality of life. Enter the Autoimmune Protocol (AIP) diet.

While no diet offers a complete cure for autoimmune conditions, the AIP diet may reduce inflammation in the gut and improve autoimmune symptoms. So, what is an autoimmune diet? In this article, we’ll break down the science behind the elimination diet, discuss how it works, and cover its risks.


What Is an Autoimmune Diet?

A healthy immune system typically produces antibodies that attack harmful cells or free radicals in the body. However, the immune systems in those with an autoimmune disorder produce antibodies that attack healthy cells, resulting in a range of symptoms. Symptoms of autoimmune diseases may include fatigue, joint pain, diarrhea, brain fog, and nerve damage, to name a few.2

Autoimmune diseases can be caused by various factors, including genetic propensity, stress, infection, and medication use.3 Some individuals may also experience increased intestinal permeability, or leaky gut, caused by damage to the gut barrier. It’s believed that a leaky gut can contribute to the development of certain autoimmune conditions.

Some foods are believed to increase gut permeability, increasing your risk of developing a leaky gut and a resulting autoimmune disorder. Hence, an autoimmune protocol diet was developed. The AIP diet eliminates foods believed to trigger an immune response and replaces them with nutrient-dense foods that support a healthy gut microbiome.4

It’s typically more strict than the paleo diet, eliminating inflammatory foods like grains, nightshade vegetables, legumes, nuts, seeds, eggs, and dairy. Instead, the AIP diet prioritizes fresh fruit and veggies, minimally processed meats, herbs and spices, natural sweeteners, olive oil, and probiotic-rich foods.

How Does an Autoimmune Diet Work?


The AIP diet has several phases, which is why it’s often considered an extension of the paleo diet. The steps to implement the Autoimmune Protocol are very straightforward, but the effects will vary between individuals. No two bodies are the same, after all.

Because the AIP diet is so extremely restrictive, it’s best to talk with your doctor before embarking on the elimination journey. Your doctor can help you understand your medical diagnosis and navigate the treatment options available to you, assessing whether or not the Autoimmune Protocol is appropriate based on your medical history.

1. Elimination Phase

The initial phase of the AIP diet can last as little as four weeks and up to three months. The elimination phase requires you to eliminate medications, foods, and additives that are believed to trigger intestinal inflammation and cause an imbalance in your gut microbiome. During this phase, you will eliminate:

  • Refined sugars
  • Grains
  • Legumes
  • Gluten
  • Food additives (emulsifiers, artificial sweeteners like stevia, and thickening agents)
  • Eggs
  • Dairy products
  • Nuts
  • Seeds
  • Caffeine
  • Alcohol
  • Canola oil
  • Almond flour

Permitted foods during this phase include:

  • Minimally processed vegetable oils (e.g., olive oil, coconut oil, and avocado oil)
  • Probiotic-rich foods (ex: dairy-free kefir, kombucha, unpasteurized sauerkraut, and fermented vegetables)
  • Fresh fruits (e.g., bananas, pears, apples, berries, and melons)
  • Vegetables
  • Minimally processed meats (e.g., grass-fed beef and organ meats)
  • Fresh herbs and spices
  • Natural sugars (e.g., honey and maple syrup)
  • Avocado
  • Bone broth

These dietary changes may seem overwhelming at first glance. However, the efficacy of the Autoimmune Protocol diet requires a thorough understanding of your response to the food groups. During this phase, you’ll cut this list of foods out of your diet entirely and all at once. Then, over the next four weeks, monitor your chronic inflammatory symptoms.

By the end of the elimination phase, you should notice an improvement in your symptoms and feel better overall. Still, this eating pattern is not sustainable longer. You will eventually need to reintroduce foods back into your diet.

2. Reintroduction Phase

During the next phase, you will gradually reintroduce the foods you eliminated into your diet. Foods must be reintroduced one at a time, allowing you to assess your tolerance and identify the foods contributing to your inflammation symptoms.

You can reintroduce foods one of two ways:

  • Reintroduce the foods, starting with the foods you miss the most
  • Reintroduce foods that offer the most impactful health benefits

When you reintroduce a food, plan to sample it several times during the first day. Start with a small amount and wait 15 minutes to monitor any potential symptoms. If you have an immune response, stop eating that food and avoid it going forward.

However, if you don’t have a response, try a larger sample size next time and gradually increase your portion until you’ve consumed a standard serving size. If you don’t have any reactions, avoid eating that food or reintroducing any other foods for five to seven days. After that, you can fully introduce the food back into your diet.

3. Maintenance

During the last phase of the AIP diet, you will take everything you learned from the previous two stages and develop a long-term, sustainable plan that fits your needs. During the maintenance phase, your aim is to embrace diet flexibility and food diversity.4

If certain foods cause unwanted symptoms, you may need to avoid them altogether. Others may be tolerated in small portions. If you haven’t already, seeking guidance from a registered dietitian nutritionist may be beneficial to ensure you employ this last phase safely and effectively.

<p class="pro-tip"><strong>Learn More: </strong><a href="atkins-vs-keto">Keto vs. Atkins Diets: Differences, Similarities, and Which One Is Best</a>.</p>

10 Conditions That Autoimmune Nutrition Might Help

There is a need for continued research to better understand the diet’s impact on specific disorders. However, dozens of autoimmune conditions may benefit from an anti-inflammatory diet plan.

These may include:

  • Celiac Disease: Celiac disease is characterized by an immune response to gluten, a protein found in wheat and other grains
  • Type 1 Diabetes: Type 1 diabetes is a life-long autoimmune disease in which your pancreas doesn’t make enough insulin. It’s typically managed with insulin injections and routine blood sugar monitoring
  • Lupus: Lupus is best defined as an autoimmune disorder in which the body’s immune system attacks its own healthy tissues and organs
  • Multiple Sclerosis: Multiple sclerosis, or MS, is an autoimmune disease that causes damage to the nerve cells, eventually leading to other concerns, such as vision problems, poor balance, and muscle weakness
  • Hashimoto’s Thyroiditis: Hashimoto’s disease is characterized by lower-than-normal thyroid levels in the body, leading to fatigue, constipation, and weight gain
  • Rheumatoid Arthritis: Rheumatoid arthritis is characterized by an immune system that attacks the joints on both sides of the body. Treatment options typically involve lifestyle changes, nutrition therapy, and physical therapy
  • Psoriasis: Psoriasis is best known for the red, itchy, scaly rash that forms on the skin, typically on the knees, elbows, trunk, and scalp
  • Crohn’s Disease: Crohn’s disease is an inflammatory bowel disease that causes swelling in the digestive tract, potentially leading to abdominal pain, diarrhea, weight loss, and malnutrition
  • Adrenal Fatigue: Adrenal fatigue typically occurs when the body is exposed to chronic stress, leading to tiredness, body aches, sleep disturbances, and digestion problems
  • Ulcerative Colitis: Ulcerative colitis, or UC, is an inflammatory bowel disease that affects the innermost lining of your large intestine or colon

Of course, it’s important to remember that dietary changes do not replace routine medical care. If you have questions about nutrition’s role in managing a chronic autoimmune disorder, seek guidance from your doctor or registered dietitian.

Risks of The Autoimmune Protocol Diet to Consider


The AIP diet may offer relief to those who experience autoimmune flare-ups of chronic inflammation. However, this autoimmune cleanse presents significant risks, especially in certain populations. The AIP diet is extremely restrictive and may contribute to serious health issues in the long run when not implemented properly.

The strict elimination diet reduces your overall intake, meaning you’re at risk of falling short of your macronutrient needs. Without sufficient carbohydrates, you may experience a decrease in energy and mental focus, while falling short of your protein needs can result in muscle loss and poor wound healing.

Avoiding major food groups or limiting your intake for weeks to months can cause undesired weight loss, cardiovascular stress, and fatigue, among other concerns. Those who are underweight, pregnant, or malnourished should not try the Autoimmune Protocol diet.

Autoimmune Protocol Diet: Is It Good for You?

While many people have seen significant improvements in their inflammation symptoms while on AIP meal plans, it’s important to remember that they are part of a highly restrictive diet; unfortunately, these types of diets aren’t exempt from potential risks. The AIP diet requires alarming restrictions, putting you at risk for malnutrition as you cut whole foods and other ingredients from your diet.

Managing an autoimmune disorder requires a multi-faceted approach and is best addressed under the guidance of credentialed healthcare professionals. Before starting a diet with the hope of improving symptoms, talk with a registered dietitian who is well-versed in gut health and its role in overall wellness. Remember that no diet can cure autoimmune conditions. Instead, they help relieve symptoms as you pursue the quality of life you deserve.

Learn How to Improve Your Nutrition and Monitor Your Glycemic Index Levels With Signos’ Expert Advice.

The roadmap to your best health takes you on an individualized journey influenced by many factors. While restrictive diets like the Autoimmune Protocol diet may offer relief, they can be difficult to maintain across your lifetime—not to mention that they present significant risks at the moment.

Health tools that track specific markers can help you make informed decisions that serve you well. Signos’ continuous glucose monitoring can improve health and encourage healthy eating habits by helping you keep track of your diet and its impact on your blood sugar levels.

Learn more about how Signos works and read up on how Signos can improve your health as you strive to reduce inflammation in the body. Not sure if Signos is a good fit for you? Find out by taking a quick quiz!

<p class="pro-tip"><strong>Also Read: </strong><a href="volumetrics-diet">Volumetrics Diet and Weight Loss: Pros & Cons</a>.</p>

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Topics discussed in this article:


  1. Chandrasekaran A, Molparia B, Akhtar E, et al. The Autoimmune Protocol Diet Modifies Intestinal RNA Expression in Inflammatory Bowel Disease. Crohns Colitis 360. 2019;1(3):otz016. doi:10.1093/crocol/otz016
  2. Lee KH, Ahn BS, Cha D, et al. Understanding the immunopathogenesis of autoimmune diseases by animal studies using gene modulation: A comprehensive review. Autoimmun Rev. 2020;19(3):102469. doi:10.1016/j.autrev.2020.102469
  3. Wang L, Wang FS, Gershwin ME. Human autoimmune diseases: a comprehensive update. J Intern Med. 2015;278(4):369-395. doi:10.1111/joim.12395
  4. Konijeti GG, Kim N, Lewis JD, et al. Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease. Inflamm Bowel Dis. 2017;23(11):2054-2060. doi:10.1097/MIB.0000000000001221

About the author

Chelsea Rae Bourgeois is a registered dietitian nutritionist with several years of experience working in the clinical setting. Once a track and field athlete on a competitive stage, she now finds joy in combining her passions as a health writer to help people embrace their wellness through nutrition and fitness.

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