Could changing what you eat help calm an overactive immune system and ease the burden of autoimmune diseases? Autoimmune diseases encompass more than 80 conditions, including inflammatory bowel disease, rheumatoid arthritis, celiac disease, lupus, hashimoto’s thyroiditis, grave’s disease, multiple sclerosis, and more. These illnesses do not have a known cure, largely because the immune system is so complex that scientists do not have the tools to safely stop the body from attacking its own tissues. As a result, treatment focuses primarily on managing autoimmune symptoms and improving quality of life. With proper treatment, there is a possibility of remission. Research and anecdotal evidence suggests that dietary strategies may play a role in reducing symptom severity. This article discusses the Autoimmune Protocol Diet (AIP diet) as one possible intervention to support individuals living with autoimmune conditions.

How does the AIP Diet Work?

The Autoimmune Protocol (AIP) diet is designed to minimize exposure to potentially pro-inflammatory foods that could contribute to immune system activation or dysregulation. The clinical implementation involves a six-week elimination phase followed by a structured reintroduction phase and maintenance period that is described below. The goal of the AIP diet is to improve symptoms and enhance the quality of life for individuals living with autoimmune conditions. This diet can be modified to the individual as needed. 

Phase 1: Elimination

The elimination phase of the AIP diet lasts for six weeks and involves minimizing exposure to certain foods that can potentially trigger inflammation. These typically include nightshade vegetables, grains, refined sugars, eggs, nuts, seeds, food additives, and certain oils. The rationale is that those foods can alter the microbiome, increase inflammation, disrupt gut lining integrity, and potentially activate an autoimmune response in individuals who are genetically susceptible, worsening chronic systemic inflammation. By removing these potential triggers, the elimination phase reduces inflammation and immune response, creating a baseline for identifying trigger foods that may worsen or alleviate autoimmune symptoms.

Phase 2: Reintroduction Phase

The reintroduction phase involves gradually adding back eliminated foods with the goal of identifying which foods trigger inflammation. Possible reactions may include gastrointestinal symptoms (abdominal pain, bloating, diarrhea, nausea), joint pain, fatigue, brain fog, insomnia, acne, skin rashes, headaches, or other flares of autoimmune disease activity. These symptoms can significantly impact quality of life because they can pose physical, mental, emotional, social, and financial limitations. For example, unpredictable gastrointestinal symptoms may make traveling stressful or difficult, while chronic fatigue or pain may affect work performance or ability to maintain a job. The AIP diet can support greater stability and expand the freedom to make everyday choices with fewer risks by helping individuals recognize and manage their dietary triggers.

Phase 3: Maintenance Phase

The maintenance phase includes transitioning to a personalized long-term diet. This stage incorporates nutrient-dense foods that were well-tolerated during the reintroduction phase, while continuing to avoid the foods that provoked symptoms or immune activation. This individualized approach supports balance, reduces chronic inflammation, and helps promote gut health by encouraging sustainable habits tailored to each person’s needs. When following the AIP maintenance diet long-term, it can be helpful to work with a dietitian to ensure you are still meeting nutritional needs through the foods included in your diet, or supplementing to make up for any components that are lacking.

AIP Diet Food List

A central component of the autoimmune protocol diet is knowing which foods to avoid and which to prioritize. The goal is to reduce exposure to foods that may worsen autoimmune response while emphasizing nutrient-dense whole foods that support gut health and reduce inflammation.

Foods to avoid: Grains, legumes, dairy, eggs, nuts and seeds, nightshade vegetables, processed foods, refined sugars such as corn syrup, cane sugar, and brown rice syrup, artificial sweeteners, processed vegetable oils, seed oils, and alcohol.

Foods to include: Fresh vegetables, leafy greens, fresh fruits, grass-fed beef, poultry, fish, shellfish, organ meats, bone broth, fermented foods, herbs, and spices. Using natural sweeteners such as maple syrup in moderation can be part of a balanced diet.

By removing potentially triggering and unhealthy foods and focusing on nutrient-dense foods, the AIP diet seeks to create a dietary foundation that reduces inflammation, improves the gut microbiome, helps heal leaky gut, supports overall health, and helps individuals regain a greater sense of control over their symptoms.

Book an Appointment With an Autoimmune Dietitian

The evidence supporting the efficacy of the Autoimmune Protocol (AIP) diet is currently limited, with most findings coming from small, uncontrolled studies and mechanistic reviews in clinical nutrition. Larger, well-designed clinical trials are still needed to confirm long-term effectiveness and safety across diverse autoimmune disorders. However, clinical experiences and anecdotal evidence does show improvement in symptoms for many individuals. With any elimination diet, it is essential to work with a registered dietitian to follow the protocol safely and strategically. Without proper guidance, the autoimmune protocol can increase the risk of nutrient inadequacies and overall dietary imbalance, making professional oversight especially valuable for sustaining a healthy, balanced diet plan.