A Guide to the AIP Diet For Beginners

If you live with autoimmune symptoms and have yet to find relief from Paleo or a low-FODMAP eating regimen, you may be wondering whether the AIP diet is worth trying.

The Autoimmune Protocol (AIP) diet is considered a more targeted elimination diet designed to reduce immune activation by removing common dietary triggers. For some people, it can help calm symptoms like digestive discomfort, joint pain, fatigue, and brain fog–areas where less restrictive diets tend to fall short in helping achieve relief.

That said, AIP is not a first-line diet in our clinic. We typically recommend starting with Paleo or low-FODMAP and then considering AIP as a next step if symptoms persist.

This beginner’s guide walks you through: How the AIP diet works, what foods are typically included and excluded, the recommended timeframe, and how to reintroduce foods safely to avoid being stuck in the restriction phase long term.

Is the AIP Diet Right for You?

The AIP diet may be worth considering if:

• You have been diagnosed with an autoimmune condition and continue to have symptoms despite trying Paleo or low-FODMAP
• Your symptoms appear to be food-responsive (digestive flares, joint pain, fatigue after eating)
• You’re willing to follow a short-term elimination diet with a clear reintroduction plan

The AIP diet may not be the best fit for you if:

• You already struggle with restrictive eating
• Your symptoms haven’t resolved with previous dietary eliminations
• You find it difficult to reintroduce foods or maintain nutritional variety (a colorful, diversified diet)

In our experience at the Ruscio Clinic, most people will know within 2–3 weeks if the AIP diet is offering relief.

What are Autoimmune Diseases and What Causes Them?

Autoimmune diseases occur when overactive immune systems mistakenly attack the bodily tissues. Women, or assigned female at birth (AFAB), 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 impacted, symptoms can vary. You may experience: Fatigue, skin rashes, bloating and abdominal pain, other chronic pain, and thyroid health issues.

Genetics, previous infections, environmental toxins, poor nutrition, and high stress levels are all potential factors behind many cases of autoimmunity 2 3. 

Disruptions to the gut microbiota may also play a major role in the development of autoimmune conditions 3 4. Out-of-balance gut bacteria can increase intestinal permeability, or “leaky gut” 5, which can trigger chronic inflammation that may give rise to autoimmune diseases 6 7. 

The good news: When you gradually 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 overall 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 addressing underlying inflammation and poor gut health. By eliminating potential dietary triggers, the AIP diet may reduce the severity of symptoms in certain 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 similar to what humans were eating in Paleolithic times (the Stone Age), can ease autoimmune symptoms. 

And when Paleo isn’t enough, a low-FODMAP diet—which limits fermentable carbohydrates that can be poorly tolerated and contribute to gas and bloating—may help.

The AIP diet takes things a step further. Similar to the Paleo diet, it reduces pressure on the gut by removing 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 diseases. For example, the AIP recommends removing nightshade vegetables, nuts, seeds, eggs, and certain spices 8 9.

Core Principles of an AIP Diet Plan

While there are different approaches to the AIP diet, there’s no established way to approach it. However, I’ll share with you some core principles that I encourage my clients who are also trying AIP to incorporate: 

• 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.

AIP 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 food groups to eliminate at first 9:

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. In my experience, clients who have already tried Paleo or a low-FODMAP diet have often eliminated many foods, so transitioning to AIP is usually not a dramatic additional step.

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 following table shows a detailed list of which foods to eat and avoid as the first step:

A Less Restrictive Version Might Also Work

Some practitioners working with the AIP diet advocate a less restrictive elimination phase that doesn’t cut out:

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

Feedback from the AIP community indicates that keeping these food items is 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, the same outcome occurs. If they aren’t seeing any symptom improvement after 2–3 weeks, it is likely that their symptoms aren’t related to the removed foods. Other pathways will then be considered.

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

AIP Stage 2: Reintroduction 

Once symptoms start to improve on the AIP diet during the elimination phase, you can consider reintroducing foods. During this phase, eliminated foods are added one at a time while carefully 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 they miss the most. 
• Keep a diary of what they added again and any symptoms that follow to identify patterns.
• If they see a food causing symptoms, take it back out of the lineup for a little while longer. But I want to make sure they don’t feel discouraged by a symptom flare! It doesn’t mean they have to avoid that food forever. Try reintroducing it again after a few weeks.
• If they eat a food without having symptoms, then I encourage them to include it in their meals again. This leads to creating a new diet that works best for them.

AIP 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, all while supporting overall health.

Admittedly, there is some trial and error involved in this phase. The foods and amounts you can tolerate may fluctuate or change over time, requiring periodic adjustments. 

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

What Does Research Say About the AIP Diet?

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

• In people with Hashimoto’s thyroiditis, following the AIP diet for 10–12 weeks was associated with improvements in quality of life, mental well-being, stress levels, and symptom burden, along with meaningful reductions in inflammation 10 11.
• Similarly, individuals with active inflammatory bowel disease (IBD) experienced improvements in quality of life after 11 weeks on an AIP-style elimination diet, with some studies also reporting improved disease activity scores and signs of mucosal healing on follow-up endoscopy 9 12.

It’s important to mention that these were small, non-randomized studies, meaning they cannot confirm that the diet itself 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.

Support also comes from research on dietary patterns similar to the AIP diet, particularly Paleo-style interventions. Meta-analyses in people with multiple sclerosis have found that Paleo-based diets, including the Wahls protocol (a Paleo variant designed to reduce symptoms of autoimmunity), were associated with greater reductions in fatigue and improvements in physical and mental quality of life compared to several other dietary approaches 13 14.

Challenges and Considerations

Before embarking on an AIP diet plan, you should be aware of the potential downsides and how to avoid or minimize them.

1. 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 15. This is why I recommend consulting a healthcare provider or dietitian before beginning.

2. Commitment Challenges

Maintaining the AIP dietary restrictions can be challenging. But successfully transitioning to both the reintroduction and maintenance phases is essential to creating a sustainable, long-term 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 think it’s important to remind clients that the AIP diet may not work for everyone, but there are plenty of other options we can explore together. Knowing they can reassess after 2–3 weeks if they are not obtaining the results they want often helps them feel more relaxed and empowered to find the right fit for them.

Tips for Success

Making any major dietary change can feel overwhelming at first. To make the AIP diet plan more successful for beginners, I encourage my clients 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. 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 with them. This reduces the stress of meal prepping and planning.
• Plan meals and snacks in advance to avoid unintentional slip-ups during the elimination phase. Clearing 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. This will help you potentially see improvements faster and yield 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 16. 
• Support your immune system with plenty of sleep, gentle outdoor activity, and focusing on other destressing 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 improve, the elimination phase is often continued until progress plateaus, which then can be followed by structured reintroduction.

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?

Yes, if followed long-term without reintroduction of diversified foods. This is why the AIP diet should be temporary and ideally guided by a clinician.

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 10. 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, it’s unlikely that the eliminated foods are the primary drivers of symptoms. Other approaches may be more appropriate to consider then.

The AIP Diet Plan: The Effort Could Be Worth It

The Autoimmune Protocol diet is a structured approach for managing autoimmune diseases, with growing evidence to support it. If you are one of many people who haven’t yet found relief with other dietary strategies, the AIP has the potential to improve your symptoms and overall quality of life. 

It’s important to note that success with the AIP diet plan requires commitment, patience, careful monitoring, and personalized adjustments during each individual phase.

Consulting a healthcare provider is especially important for tailoring this diet to your individual needs and ensuring you get enough nutrients through diversified food consumption. 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.

The Ruscio Institute has developed a range of high-quality formulations to help our clients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you. The information on DrRuscio.com is for educational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.

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.