A Guide to the AIP Diet For Beginners

If you live with autoimmune symptoms and have yet to find relief from other healthy elimination-style diets that remove inflammatory foods, you may be wondering whether the AIP diet is worth trying.

This beginner’s guide covers how the AIP diet works, which foods are included and excluded, how long to follow it, and how to reintroduce foods thoughtfully so you don’t stay overly restricted long term.

What is the AIP Diet? 

The Autoimmune Protocol (AIP) diet is a targeted elimination diet designed to reduce immune activation. Unlike many other elimination diets, it goes beyond removing ultra-processed foods and refined sugars and also excludes foods that may be more likely to provoke immune or inflammatory responses in people with autoimmune disease, such as nightshade vegetables, nuts, seeds, eggs, and certain spices.

By eliminating potential dietary triggers, the AIP diet may help reduce symptom severity in some autoimmune conditions, including Hashimoto’s thyroiditis, inflammatory bowel disease (IBD), rheumatoid arthritis, and lupus. 

The AIP diet is often considered a more structured extension of the Paleo diet. While many people experience symptom relief with Paleo alone, AIP is sometimes used when additional food eliminations are needed to clarify triggers.

The core principles of the AIP diet plan are to:

• Focus on nutrient-dense foods: It’s easy to be so focused on removing trigger foods that you forget to focus on high-quality and diversified nutrition. It’s important to ensure the remaining foods in your diet are highly nutritious. Examples are high-quality meats (especially organ meats), wild-caught fish, vegetables, berries, and healthy fats.
• Don’t stay highly restricted: When you experience long-awaited symptom relief on a restricted diet like AIP, you may be hesitant to reintroduce foods that might trigger symptoms again. Even though it may feel counterintuitive, it’s important to systematically reintroduce foods to identify which ones do (or don’t) create symptoms. Otherwise, you may find yourself stuck with a very restricted diet that can be nutritionally poor and socially limiting.
• Personalize and maintain: The ultimate goal is to create a long-term, sustainable diet tailored to your individual needs and tolerances.

How Does the AIP Diet Help Autoimmunity? 

Disruptions in the gut microbiota and increased intestinal permeability, or “leaky gut”, are associated with chronic inflammation and immune activation in autoimmune conditions 1 2 3 4 5. 

When you gradually remove inflammatory foods with the AIP diet, inflammation decreases, and the gut microbiota can recover. 

Research on the AIP diet is in its infancy, but there are some encouraging initial studies. For example, those with Hashimoto’s who followed the AIP diet for 10-12 weeks saw improvements in quality of life, mental well-being, stress, symptom burden, and inflammation levels 6 7. Similarly, patients with inflammatory bowel disease (IBD) experienced improvements in quality of life after 11 weeks on an AIP-style elimination diet 8 9.

While more research is needed, these findings, along with our clinical experience, support using the AIP diet as a short-term, symptom-guided approach.

AIP Diet Stage 1: Elimination

The AIP diet restricts a broad range of foods during the elimination phase. This helps the diet have a large positive impact on immune activation and inflammation in the long run. 

Here are the main food categories to eliminate at first 8:

1. Grains and legumes: wheat, barley, rice, corn, soybeans, lentils, and peanuts
2. Dairy products: such as milk, cheese, yogurt, butter, and cream
3. Nightshade vegetables: such as tomatoes, potatoes, eggplant, peppers, and spices like paprika and cayenne
4. Nuts and seeds: such as almonds, cashews, sunflower seeds, sesame seeds, and chia seeds
5. Eggs: including yolks and whites
6. Ultra-processed foods: high-sugar, refined, and fast foods, especially those with additives like emulsifiers and artificial sweeteners
7. Coffee and alcoholic beverages

Some people choose to transition to the elimination phase gradually, cutting out a couple of foods at a time. Others make the switch quickly—over a weekend to reduce routine disruption, for example. 

Ideally, you’ll work with a practitioner who’s familiar with the AIP diet and they can help you understand what is best for you. 

AIP Diet Plan for Beginners: Food List for the Elimination Stage

During the elimination phase, the AIP diet focuses on nutrient-dense whole foods while removing common immune triggers.

The table below shows a more detailed breakdown of foods to eat and avoid during the elimination phase:

AIP Diet Stage 2: Reintroduction 

Once symptoms begin to improve during the elimination phase, the next step is reintroducing foods in a structured, intentional way.

The goal of reintroduction is to identify which foods you tolerate well and which may still contribute to symptoms, so your diet can expand safely over time.

A Simple, Practical Reintroduction Framework:

• Step 1: Choose one food to test at a time. Avoid introducing multiple new foods at once.
• Step 2: Start with a small portion. This lowers the chance of a strong reaction and makes symptoms easier to interpret.
• Step 3: Increase to a normal serving if no symptoms occur. This helps confirm tolerance under real-world conditions.
• Step 4: Wait 3–5 days before introducing another food. Delayed reactions are common, so spacing matters.
• Step 5: Monitor symptoms, not perfection. If symptoms appear, remove the food and plan to retry it later.

To help patients navigate this phase more confidently, I often recommend:

• Starting with foods you miss most or that meaningfully improve diet variety. Reintroducing these foods first can make the process feel more sustainable and improve adherence, especially during the early stages.
• Keeping brief, consistent notes on what was reintroduced and how you felt afterward. This helps identify patterns that might be missed if symptoms are assessed retrospectively.
• Reintroduce foods under typical day-to-day conditions. High stress, poor sleep, or illness can make it harder to interpret reactions accurately.

A symptom flare during reintroduction doesn’t mean a food needs to be avoided forever. In many cases, it simply signals that your system isn’t ready for that food yet. Reintroducing it again after a few weeks often leads to a different outcome.

If you tolerate a food without symptoms, you can include it back into your regular meals. Over time, this process helps you build a personalized diet that supports symptom control without unnecessary restriction.

For step-by-step guidance, download our Food Reintroduction Guide. It can help make this process clearer and less overwhelming.

AIP Diet Stage 3: Maintenance 

The maintenance phase is where the AIP diet becomes your diet. The goal is to settle into a personalized, nutrient-dense way of eating built around the foods you tolerate well, while continuing to minimize autoimmune flare-ups and support overall health.

Foods that still trigger symptoms may need to stay out a bit longer as healing continues, and that’s okay. Over time, many people are able to expand food variety as their system becomes more resilient. If meaningful food freedom remains difficult to achieve, it may be a sign that additional support beyond diet alone could help move things forward.

This personalized, maintenance-focused approach is also reflected in emerging research examining how AIP-style diets affect symptoms and quality of life in autoimmune disease.

Tips for Success

To make the AIP diet plan more successful for beginners, I encourage my patients to try these tips that you may find useful as well:

• Find a few tasty and nutritious basic recipes and develop a simple meal plan. Autoimmune Wellness is a great resource for delicious AIP recipes.  
• Make a few big batches of simple starter recipes and load up your freezer with them. This reduces the stress of meal prepping and planning.
• Clear your pantry of non-AIP foods and stocking up on AIP-friendly ingredients will help during this time.
• Be as strict as possible about the diet during the first 2–3 weeks. But don’t let perfect be the enemy of the good. Even about 80% adherence during the early phase may still lead to meaningful symptom improvement.
• Get support. Joining AIP-focused communities and working with a healthcare professional can provide guidance, connectedness, and motivation.
• In addition to dietary changes, targeted probiotic support may help regulate immune signaling and gut health 10.
• Support your immune system with plenty of sleep, gentle outdoor activity, and focusing on other stress-reducing activities such as meditation and deep breathing.

Frequently Asked Questions About the AIP Diet

How long should you follow the AIP diet?

Most people know within 2–3 weeks whether the AIP diet is helping. If symptoms begin to improve, the elimination phase is often continued until progress plateaus before moving into structured reintroduction.

In clinical studies, AIP-style diets have typically been followed for about 10–12 weeks 6 7. This reinforces that AIP is intended as a time-limited, symptom-guided approach, not a permanent way of eating.

Is the AIP diet better than Paleo?

AIP is more restrictive than Paleo. Paleo is often effective on its own, and we generally recommend trying it first before moving to AIP.

Can the AIP diet worsen nutrient deficiencies?

The restrictive nature of elimination diets like the AIP may sometimes worsen deficiencies in essential nutrients like calcium, vitamin B1, and vitamin B12 if not carefully planned 11. This is why I recommend consulting a healthcare provider or dietitian before beginning.

Does the AIP Diet Lower Autoimmune Antibodies?

Not always.

Research on the AIP diet and autoimmune antibody levels is limited and mixed. In one small study of people with Hashimoto’s thyroiditis, symptoms and quality of life improved after 12 weeks on the AIP diet, even though thyroid peroxidase (TPO) antibody levels increased 6. This suggests that symptom relief does not always correspond to positive changes in antibody levels.

For comparison, some research indicates that less restrictive approaches, such as a standard Paleo diet, may be more likely to reduce thyroid antibodies in certain autoimmune thyroid conditions.

Because of this, we don’t use antibody levels alone to judge whether the AIP diet is “working”. Instead, we view AIP as a short-term, symptom-guided tool and reassess its value during the reintroduction and maintenance phases.

What if the AIP diet doesn’t help?

If symptoms don’t improve after 2–3 weeks, the eliminated foods are less likely to be the primary drivers of symptoms. At that point, other approaches may be more useful to explore. Working with a practitioner who’s experienced in autoimmunity can help identify the next most appropriate steps.

The AIP Diet Plan: The Effort Could Be Worth It

The Autoimmune Protocol diet is a structured, short-term approach used to help identify dietary triggers and reduce autoimmune-related symptoms. While research is still emerging, both clinical studies and real-world experience suggest that AIP may improve symptoms and quality of life for some people, especially when other dietary strategies have fallen short.

Success with the AIP diet depends on thoughtful implementation. This includes committing to the elimination phase, monitoring symptoms carefully, and moving through reintroduction and maintenance in a personalized way rather than staying overly restricted.

Because AIP is a targeted and restrictive diet, working with a qualified healthcare provider can be helpful for tailoring the approach to your individual needs and ensuring nutritional adequacy. If you would like guidance on using the AIP diet or support for autoimmune-related concerns, our clinic team is here to help.

Dr. Michael Ruscio is a DC, natural health provider, researcher, and clinician. He serves as an Adjunct Professor at the University of Bridgeport and has published numerous papers in scientific journals as well as the book Healthy Gut, Healthy You. He also founded the Ruscio Institute of Functional Health, where he helps patients with a wide range of GI conditions and serves as the Head of Research.