The Autoimmune Protocol diet: How nutrition can help manage autoimmune conditions

The Autoimmune Protocol (AIP) diet has been shown to help reduce symptoms of autoimmune disease. Learn more about what it is here.

Autoimmune diseases occur when the immune system mistakenly attacks healthy cells, tissues, or organs in the body. While there is no cure for autoimmune diseases, managing them with a comprehensive approach that includes nutrition can be beneficial. 

The Autoimmune Protocol (AIP) diet is one such approach that focuses on removing potentially inflammatory foods and supporting gut health to alleviate symptoms and improve overall well-being. In this article we will be reviewing:

  • Why is addressing underlying inflammation important when it comes to autoimmune conditions? 
  • What is the Autoimmune Protocol (AIP) diet? 
  • What foods am I allowed to eat with the AIP diet? Which should I avoid?
  • Is the AIP diet forever? 

Understanding autoimmune conditions and inflammation

Autoimmune diseases are characterized by immune dysfunction and chronic inflammation. Certain foods can trigger or exacerbate inflammation (and subsequently an immune response and symptom flares) in individuals with autoimmune diseases.

The Autoimmune Protocol (AIP) diet

The AIP diet is an elimination diet that aims to remove potential triggers of inflammation and promote gut and overall healing. It involves removing foods that are commonly associated with food sensitivities, allergies, or that have the potential to promote inflammation. 

Like other elimination diets, the AIP diet is not intended to be forever. After several weeks of an elimination phase, a re-introduction phase will help you understand which specific foods and food groups may be triggers for your symptoms. If you would learn mroe about how to do an elimination diet safely, check out this article!

Foods to avoid on the AIP diet during the initial elimination phase include:  

  • Gluten (e.g., Bread, pasta, and other wheat-containing products) 
  • Grains (e.g., Quinoa, barley, brown and white rice)
  • Legumes (e.g., Chickpeas, black beans, navy beans, lentils)
  • Dairy
  • Eggs
  • Nuts 
  • Seeds 
  • Nightshade vegetables (e.g., Toamtoes, eggplant, potatoes, peppers) 
  • Seed and vegetable oils 
  • Processed foods
  • Refined sugars
  • Alcohol
  • Sugar alcohol 

Research has shown that the AIP diet can have an impact on reducing systemic inflammation and overall symptoms for autoimmune conditions such as inflammatory bowel disease (i.e., colitis, Crohn’s), Hashimoto’s thyroiditis, and rheumatoid arthritis (1, 2, 3).

It's important to note that while some studies have shown positive results, more research is needed to establish the effectiveness of the AIP diet for each specific autoimmune conditions. More research, including larger and controlled studies, is needed to further explore the effectiveness of the AIP diet for specific autoimmune conditions.

While individual responses may vary, some potential benefits of the AIP diet for managing autoimmune diseases include:

  • Reduced inflammation: By removing potential dietary triggers, the diet may help reduce inflammation in the body.
  • Gut healing: The diet supports gut health by removing irritating and potentially damaging foods, allowing the gut to heal.
  • Identification of food sensitivities: By following an elimination and reintroduction process, individuals may identify specific food triggers that worsen their symptoms.
  • Improved nutrient intake: The emphasis on nutrient-dense foods can provide essential vitamins, minerals, and antioxidants needed for overall health and immune function.

Foods to include in the AIP diet

The AIP diet emphasizes nutrient-dense, anti-inflammatory foods that support healing and gut health. These include:

  • High-quality proteins: Grass-fed meat, organic or free range/pasture-raised poultry and eggs, wild-caught fish, and organ meats
  • Non-nightshade vegetables: Leafy greens, cruciferous vegetables, and colorful vegetables
  • Healthy fats: Avocado, olive oil, coconut oil, ghee, fatty fish
  • Fermented foods: Sauerkraut, kimchi, vinegar, and kombucha to support gut health
  • Bone broth: Rich in nutrients that support healing and gut integrity (collagen is included, too!)
  • Fruits in moderation: Low-sugar fruits like berries, which are nutrient-dense and provide antioxidants
  • Specific sweeteners: Honey and maple syrup in moderation 

Considerations and potential challenges

Having an autoimmune condition is by no means easy, and supporting your body with a specific way of eating also has its challenges. Even though the AIP diet is intended to be temporary, the elimination phase can still feel restrictive and bothersome.

Below are several things to be aware of if you are planning to pursue the AIP diet:

  • Nutrient deficiencies: The AIP diet restricts certain food groups, so it's important to ensure adequate intake of key nutrients, such as calcium, vitamin D, and omega-3 fatty acids. Supplementation or careful food selection may be necessary.
  • Social and practical considerations: Following the AIP diet may require additional planning, preparation, and adjustments in social situations. Support from healthcare professionals, dietitians, and a community of individuals following similar diets can be helpful.
  • Disordered eating triggers: Eliminating certain types of food can be triggering to some people, especially those who have a history of disordered thoughts and behaviors around food. If this sounds like you, working with a Health At Every Size (HAES) or intuitive eating-informed dietitian or nutrition specialist who has training in working with patients with disordered eating is helpful and may even be necessary. Pollie’s registered dietitians and health coaches are HAES and intuitive eating-informed.


While the AIP diet may be beneficial for managing autoimmune diseases, it's important to remember that individual responses may vary and this diet may not be for everyone. 

It's advisable to consult with a healthcare professional or registered dietitian before starting any dietary changes. Especially with a more structured way of eating like this, working with a specialist who has a background in helping patients cultivate a healthy and positive attitude toward using food as medicine is advised, and can make an experience that may seem rigid and limiting at first turn into something that is fulfilling and sustainable. 


  1. ​​Chandrasekaran A, Molparia B, Akhtar E, Wang X, Lewis JD, Chang JT, Oliveira G, Torkamani A, Konijeti GG. The Autoimmune Protocol Diet Modifies Intestinal RNA Expression in Inflammatory Bowel Disease. Crohns Colitis 360. 2019 Oct;1(3):otz016. doi: 10.1093/crocol/otz016. Epub 2019 Jul 12. PMID: 32309803; PMCID: PMC7147823.
  2. Abbott RD, Sadowski A, Alt AG. Efficacy of the Autoimmune Protocol Diet as Part of a Multi-disciplinary, Supported Lifestyle Intervention for Hashimoto's Thyroiditis. Cureus. 2019 Apr 27;11(4):e4556. doi: 10.7759/cureus.4556. PMID: 31275780; PMCID: PMC6592837.
  3. Vadell AKE, Bärebring L, Hulander E, Gjertsson I, Lindqvist HM, Winkvist A. Anti-inflammatory Diet In Rheumatoid Arthritis (ADIRA)-a randomized, controlled crossover trial indicating effects on disease activity. Am J Clin Nutr. 2020 Jun 1;111(6):1203-1213. doi: 10.1093/ajcn/nqaa019. PMID: 32055820; PMCID: PMC7266686.