What are the phases of the AIP diet?

November 5, 2025 •

4 min read

According to research published in the journal Nutrients, the autoimmune protocol (AIP) diet follows a structured process of elimination, reintroduction, and maintenance to help manage autoimmune conditions. Understanding what are the phases of the AIP diet? is key to identifying potential food triggers and creating a personalized, long-term eating plan for improved health and well-being.

Quick Summary

The Autoimmune Protocol (AIP) diet is an elimination and reintroduction process designed to identify individual food sensitivities. It is not intended as a permanent solution but rather a tool to help people with autoimmune conditions reduce inflammation and heal the gut lining. The protocol consists of three distinct stages: elimination, reintroduction, and maintenance, allowing for a personalized approach to dietary management.

Key Points

Elimination: The first phase of the AIP diet involves the temporary removal of common inflammatory foods like grains, dairy, and nightshades for a period of 30 to 90 days to reduce inflammation.
Reintroduction: Following elimination, foods are reintroduced one at a time over several months to test for individual sensitivities and build a personalized food list.
Maintenance: The final phase is a long-term, individualized diet plan based on the results of the reintroduction phase, focusing on tolerated foods and avoiding triggers.
Not a Permanent Solution: The ultimate goal of AIP is not lifelong restriction but rather to identify triggers and create the most inclusive diet possible for long-term health.
Personalization is Key: Every individual's journey is different, and the reintroduction process is crucial for discovering which foods work best for your unique body.
Focus on Nutrient Density: Throughout the AIP process, there is a strong emphasis on consuming nutrient-dense whole foods like leafy greens, high-quality proteins, and healthy fats.

What is the Autoimmune Protocol (AIP) Diet?

The Autoimmune Protocol (AIP) is a specialized version of the Paleo diet that takes a more targeted and restrictive approach to managing autoimmune disease. It is an elimination diet designed to help reduce inflammation, heal the gut lining, and regulate the immune system by temporarily removing foods known to be common triggers of immune reactions. Once the body has had a chance to calm down, the protocol systematically reintroduces foods to determine individual tolerances. The journey is not meant to be permanent but rather a pathway to creating a personalized, sustainable diet.

The Three Core Phases of the AIP Diet

Phase 1: The Elimination Phase

This is the most restrictive part of the diet and is designed to give the immune system a rest from potential inflammatory foods. The duration of this phase is typically between 30 and 90 days, or until a person notices a significant and sustained reduction in their symptoms. Consistency is crucial during this time to effectively reset the body and prepare for the next step. If no improvements are seen after 90 days, it is often recommended to troubleshoot with a healthcare professional, as other factors may be at play.

Foods to Eliminate During the AIP Elimination Phase:

Grains: All grains, including gluten-free varieties like corn, rice, and quinoa.
Legumes: Beans, lentils, peas, soy, and peanuts.
Nightshade Vegetables: Tomatoes, potatoes, peppers, and eggplant.
Dairy: Milk, cheese, butter, and yogurt.
Eggs: Both egg whites and yolks are removed due to potential sensitivities.
Nuts and Seeds: This includes seed-based spices like mustard and cumin.
Refined Sugars and Processed Foods: High-fructose corn syrup, artificial sweeteners, and food additives.
Alcohol and Coffee: These are eliminated entirely to reduce their impact on the immune system.

Focus on Nutrient-Dense Foods: In place of the eliminated items, the diet emphasizes consuming nutrient-dense, whole foods to support healing. This includes:

High-quality meats and organ meats
Wild-caught fish and shellfish
A wide variety of vegetables (excluding nightshades)
Moderate amounts of fruit
Healthy fats like coconut, olive, and avocado oil
Fermented foods like sauerkraut and kombucha
Bone broth

Phase 2: The Reintroduction Phase

Once symptoms have stabilized or improved, individuals can begin the methodical process of reintroducing eliminated foods one by one. This phase is key to personalizing the diet, as not everyone reacts negatively to the same foods. This is an opportunity to test for individual sensitivities in a controlled manner.

Reintroduction Process:

Select a Food: Choose one food to test. It's often recommended to start with those least likely to cause a reaction, such as egg yolks or ghee.
Test and Observe: On the testing day, consume a small amount of the food, wait 15 minutes to check for an immediate reaction, and then eat a slightly larger portion if no symptoms occur. Later that day, eat a normal portion.
Wait and Watch: After the testing day, avoid that food completely for 5 to 7 days. During this waiting period, monitor for any delayed symptoms, such as joint pain, fatigue, headaches, or digestive issues. This waiting period is critical because food sensitivities can have delayed reactions.
Evaluate: If no symptoms appear during the observation period, the reintroduction is successful, and the food can be reincorporated into the diet. If a reaction occurs, the food should be removed and potentially tested again in the future.
Repeat: Proceed with the next food on the list only after a successful reintroduction and observation period.

Phase 3: The Maintenance Phase

The final phase is a personalized, long-term eating plan based on the results of the reintroduction phase. The goal is to build the broadest and most nutritionally diverse diet possible without triggering symptoms. This phase emphasizes sustainability and encourages a balanced approach to eating and lifestyle. Some foods might be tolerated in small amounts or occasionally, while others may need to be avoided entirely long-term.

Comparison of AIP Diet Phases


Feature	Elimination Phase	Reintroduction Phase	Maintenance Phase
Primary Goal	To calm the immune system and promote gut healing by removing trigger foods.	To systematically identify individual food sensitivities.	To sustain a personalized diet that minimizes symptoms and supports long-term health.
Duration	30 to 90 days, or until symptoms improve.	Several months to a year, depending on the individual's pace.	Long-term; this is the final eating pattern.
Dietary Focus	Highly restricted to nutrient-dense, anti-inflammatory whole foods.	Gradually adding one eliminated food back at a time.	Incorporating all tolerated foods while permanently avoiding triggers.
Key Action	Avoid all common triggers like grains, dairy, eggs, and nightshades.	Perform methodical food challenges and monitor reactions.	Build the most varied and inclusive diet possible based on individual tolerance.

Conclusion

The Autoimmune Protocol diet is a powerful tool for those with autoimmune conditions seeking to understand and manage their symptoms through nutritional changes. It is not a permanent solution but rather a structured journey through three distinct phases: elimination, reintroduction, and maintenance. By following these phases carefully, individuals can move from a restrictive, healing period to a personalized, long-term eating pattern that supports their health and well-being. This methodical approach empowers individuals to regain control over their diet and reduce inflammation, leading to a better quality of life. For further resources and personal stories, you may want to explore the Autoimmune Wellness website for comprehensive guidance and support on your AIP journey.

Frequently Asked Questions

The duration of the elimination phase is individual, typically lasting between 30 and 90 days, or until a noticeable reduction in autoimmune symptoms is achieved. Some people may see improvements sooner, but it's important to feel stable before beginning reintroductions.

You should begin the reintroduction phase once you experience significant improvement or resolution of your autoimmune-related symptoms, which often occurs after at least 4 to 6 weeks on the strict elimination diet.

Foods should be reintroduced one at a time. A common method involves eating a small amount of the test food, waiting 15 minutes, then eating a slightly larger amount if no symptoms occur, and finally eating a normal portion. This is followed by a 5 to 7 day waiting period to monitor for any delayed reactions.

Most protocols recommend starting with foods that are least likely to cause a reaction. Common first reintroductions include egg yolks, ghee, and certain seed-based spices.

If a food causes a flare-up, you should remove it from your diet. However, your body's tolerance can change over time. You can attempt to reintroduce a previously failed food again in the future, especially after further healing has occurred.

The maintenance phase is your personalized, long-term diet. It includes all the foods you successfully reintroduced without issue and permanently excludes the ones that trigger symptoms. It focuses on dietary diversity while staying within your individual tolerance levels.

No, the AIP is not a permanent diet. Its purpose is to be a structured process for healing and identifying food sensitivities. The goal is to build a personalized, less restrictive diet for the long term, not to remain in the strict elimination phase indefinitely.