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A Guide to the AIP Diet For Beginners

Written by Dr. Michael Ruscio, DC on January 8, 2025

Written by Dr. Michael Ruscio, DC on January 8, 2025 — Reviewed by Aimee Gallo

• Autoimmune Disease|
• AIP Diet Plan|
• Elimination|
• Reintroduction|
• Maintenance|
• Studies|
• Considerations|
• Tips for Success|

Being diagnosed with autoimmune diseases, like Hashimoto’s thyroiditis or colitis, can feel overwhelming. However, elimination diets, including the autoimmune protocol (AIP) diet, may help reduce symptoms and improve quality of life.

Because of its name, people often jump to the conclusion that an AIP diet plan is the hands-down best diet for autoimmune conditions. However, starting with less restrictive diets is usually a better first step. 

At the clinic, we recommend trialing a standard Paleo diet and a low FODMAP elimination diet first. We may move on to the AIP diet if these approaches don’t ease autoimmune symptoms such as gut pain, joint pain, and brain fog sufficiently. 

Setting up an AIP diet plan can be a little daunting at first. But most of my clients adapt over time and find a version that works for them. 

If you’re considering an AIP diet for beginners, read this article to learn how to tailor it to your specific needs. 

What Is Autoimmune Disease and Why Does It Happen?

Autoimmune disease is when an overactive immune system mistakenly attacks the body’s own tissues. Women are especially vulnerable, making up more than three-quarters (78%) of people with an autoimmune disease 1. 

Depending on which part of the body is being attacked, symptoms can range from fatigue to skin rashes, bloating and abdominal pain, other chronic pain, and thyroid health issues.

Susceptible genes, infections, environmental toxins, poor nutrition, and high stress levels may be behind many cases of autoimmunity 2 3. 

Disruptions to the gut microbiota may also play a major role in autoimmune conditions 4. Out-of-balance gut bacteria can increase intestinal permeability, aka “leaky gut” 5, which can trigger chronic inflammation that may give rise to autoimmune disease 6 7. 

But when you remove inflammatory foods with the AIP or other elimination diets, the gut microbiota can recover, allowing inflammation to decrease. This may help to heal the gut lining and calm an overactive immune response, thus reducing the risk of autoimmunity.

Introducing the AIP Diet Plan for Beginners

The Autoimmune Protocol (AIP) diet is an elimination diet that has emerged as a promising intervention for managing autoimmune diseases.

It can help by reversing underlying inflammation and poor gut health. By eliminating potential dietary triggers, the AIP diet may reduce the severity of symptoms in autoimmune conditions, such as Hashimoto’s thyroiditis, inflammatory bowel disease (IBD), rheumatoid arthritis, and lupus. 

Essentially, the AIP diet is a specialized extension of the Paleo diet. Often, a standard Paleo diet, which focuses on food patterns closer to what humans were eating in Paleolithic times (the Stone Age), is enough to ease autoimmune symptoms. 

When Paleo isn’t enough, a low FODMAP diet—which reduces the fermentable carbohydrates that some gut bacteria use to make a lot of gas—can be.

The AIP diet takes things a step further. Like the Paleo diet, it removes grains, legumes, processed foods, and refined sugars. But it also eliminates other foods believed to be inflammatory or disruptive to the immune system in people with autoimmune disease. For example, the AIP removes nightshade vegetables, nuts, seeds, eggs, and certain spices.

Core AIP Diet Plan Principles

There are different approaches to the AIP diet, and there’s no established way to go about it. However, when I work with clients trying AIP, these are the core principles I encourage them to incorporate:

• Focus on nutrient-dense foods: It’s easy to be so focused on removing trigger foods that you forget to focus on good nutrition. Make sure 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 welcome symptom relief on a restricted diet like AIP, reintroducing foods that might trigger symptoms again can feel a bit scary. However, it’s important to systematically reintroduce foods to identify which ones do (or don’t) create symptoms. Otherwise, you can be stuck with a very restricted diet that may 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.

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. 

These are the food groups to eliminate at first:

1. Grains and legumes, such as 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, such as high-sugar, refined, and fast foods, especially those with additives like emulsifiers and artificial sweeteners.

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, for example. 

Ideally, you’ll work with a practitioner who’s familiar with the AIP diet and will help you work out what is right for you. In my experience, when clients have already tried the Paleo or low FODMAP diet, they have already eliminated quite a few foods, so AIP isn’t too much of an extra step.

The following table shows in more detail which foods to eat and avoid during the elimination phase.

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

A Less Restrictive Version Might Also Work

Some practitioners of the AIP diet advocate a less restrictive elimination phase that allows:

• Rice
• Pseudo-grains (quinoa, teff, millet, amaranth, or buckwheat)
• Ghee
• Legumes (except soy)
• Seeds (including coffee and cocoa) 

Feedback from the AIP community indicates that these are often not troublesome for autoimmune patients and can make the elimination phase more convenient. 

In my experience, whether clients do the traditional AIP elimination phase or a slightly more liberal version, if they don’t see any symptom improvement after 2–3 weeks, it’s likely that their symptoms aren’t related to the foods they eliminated.

But those who do notice improvement can carry on with the elimination phase until their improvements plateau. Then it’s time for reintroduction.

Stage 2: Reintroduction 

Once symptoms start to improve on the AIP diet, it’s time to start reintroducing foods. During this phase, eliminated foods are reintroduced one at a time while monitoring for symptoms. This helps identify which foods are well-tolerated and which might trigger symptoms.

In the clinic, a typical reintroduction protocol includes:

• Adding one food at a time in small quantities
• Waiting 3–5 days between reintroductions
• Recording any symptoms in a food journal

To help them ease into the process, I coach my clients to:

• Begin with the foods you miss the most. 
• Keep a diary of what you reintroduce and any symptoms that follow to make it easier to see patterns.
• If a food causes symptoms, avoid it for a while longer. But don’t feel discouraged by a symptom flare! It doesn’t mean you’ll have to avoid that food forever. You can try reintroducing it again after a few weeks.
• If you eat a food without having symptoms, you can include it in your diet again.

Stage 3: Maintenance 

The maintenance phase is all about establishing a personalized diet based on tolerated foods. This phase is about building a long-term nutritious diet that minimizes autoimmune flare-ups while supporting overall health.

There is some trial and error involved in this phase. The foods and amounts of them you can tolerate may fluctuate or change over time, requiring periodic tweaks. 

Even if you are feeling well, I recommend checking in with a dietitian or AIP coach every now and again to make sure you’re managing your symptoms while getting enough variety in your maintenance diet.

Studies of the AIP Diet

Large, conclusive studies of the AIP diet for autoimmune disease are still limited, but several small studies are encouraging. For example:

• People with Hashimoto’s thyroiditis who followed the AIP diet for 12 weeks saw improvements in their quality of life, mental state, stress levels, and chronic conditions related to Hashimoto’s 8.
• People with active inflammatory bowel disease (IBD) had better quality of life when they followed an AIP elimination diet for 11 weeks 9. 
• Women with Hashimoto’s thyroiditis reported better quality of life and fewer symptoms while using the AIP diet for 10 weeks. Their inflammation decreased impressively by about a third (29%) 10.
• IBD patients saw significantly improved IBD scores on the AIP diet, with follow-up endoscopies showing signs of mucosal healing in some cases 11.

These were small, nonrandomized studies, making it impossible to confirm that the diet caused the positive outcomes. Nevertheless, many people—both my own clients and others within the functional health and conventional medicine communities—have reported benefits that justify the AIP’s dietary restrictions.

We also have research supporting dietary interventions that are similar to the AIP diet. For instance:

• One meta-analysis (highest-quality study of studies) looked at 12 randomized controlled trials (the gold-standard type of experimental study) to see how 8 different diets affected fatigue and quality of life in people with multiple sclerosis (MS). Compared to the other seven diets—including a low-fat diet and the Mediterranean diet, which performed well—the Paleo diet showed the greatest effects in reducing fatigue and improving physical and mental quality of life in people with MS 12
• Another meta-analysis showed that the Wahls Paleo diet (a Paleo variant designed to reduce autoimmunity) has the potential to improve fatigue, mental health, and quality of life in people with MS flares 13.

Effect on Autoantibodies

So far, I’ve found only one small study that examined how the AIP diet affects levels of autoantibodies—the immune proteins that attack human tissues and are a hallmark of autoimmune conditions. A decline in autoantibodies typically indicates an improvement in someone with an autoimmune disorder.

That study found that Hashimoto’s patients who followed a 12-week AIP diet had a surprising 40% increase in thyroid peroxidase (TPO) antibodies. Usually, higher levels of TPO antibodies equate to worse symptoms, but in this study all but one person’s symptoms got better. The researchers guessed that the rise in TPO, which wasn’t even statistically meaningful, was a byproduct of unknown natural changes that happen in autoimmunity 8.  

For comparison, a small-scale systematic review (methodical account of studies) found that people with Hashimoto’s and Graves’ disease who ate a standard Paleo diet for at least 8 weeks had lower thyroid antibodies and normalized thyroid hormones 14.

In summary, there’s enough evidence to consider trying the AIP diet for an autoimmune condition. With support from a knowledgeable clinician, the AIP may be especially worth trying if other diets you’ve tried haven’t provided significant symptom relief.

Challenges and Considerations

Before embarking on an AIP diet plan, it’s a good idea to be aware of the potential downsides and how to minimize them.

1. Nutrient Deficiencies

The restrictive nature of elimination diets like the AIP can worsen deficiencies in essential nutrients like calcium, vitamin B1, and vitamin B12 if not carefully planned 15. This is why I recommend consulting a healthcare provider or dietitian.

2. Commitment Challenges

The AIP diet’s restrictive nature can be challenging to maintain. Transitioning to the reintroduction and maintenance phases is essential to creating a sustainable diet.

3. Individual Variability

Not everyone responds to the AIP diet the same. Factors such as genetics, environmental exposures, stress levels, and the severity of autoimmune symptoms may influence outcomes. 

I always try to help clients understand that this diet might not work for them, but not to despair if it doesn’t—we have other options. Many people seem to relax when they realize this and feel empowered when they know they can discontinue the diet after 2–3 weeks if it’s not offering enough benefits.

Tips for Success

Making any dietary change can feel overwhelming at first. To make the AIP diet plan more successful for beginners, I coach my clients to try these tips:

• Find a few tasty and nutritious basic recipes and use them to develop a simple meal plan. Gradually experiment with more complex dishes as you become familiar with the diet and your safe foods.
• Make a few big batches of simple starter recipes and load up your freezer. 
• Plan meals and snacks in advance to avoid unintentional slip-ups. Clearing your pantry of non-AIP foods and stocking up on AIP-friendly ingredients will help.
• Be as strict as possible about the diet during the first 2–3 weeks. This will help you feel better faster and give you better results during your food reintroductions.
• Get support. Joining AIP-focused communities and working with a healthcare professional can provide guidance, connectedness, and motivation.
• In addition to dietary changes, probiotics are natural helpers for autoimmune patients.
  • Probiotics can help reduce intestinal permeability 16 and promote a healthy immune response in your gut 17. 
  • We use a triple therapy approach in the clinic for best results.
• Support your immune system with plenty of sleep, gentle outdoor activity, and other destressing activities such as meditation and deep breathing.

The AIP Diet Plan: The Effort Could Be Worth It

The AIP diet is a structured approach to managing autoimmune diseases, with growing evidence to support it. Especially if you haven’t found relief with other dietary strategies, the AIP has the potential to improve your symptoms and overall quality of life. 

Success with the AIP diet plan requires commitment, patience, careful monitoring, and personalized adjustments during the elimination, reintroduction, and maintenance phases.

Consulting a healthcare provider is important for tailoring the diet to your individual needs and making sure you get enough nutrients. If you’d like to discuss the AIP diet, autoimmunity, or any other health concerns with one of our practitioners, please reach out to us.

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