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June 11, 2025

The Ultimate Guide to the Paleo Autoimmune Protocol (AIP) Diet

The Paleo Autoimmune Protocol (AIP) is a powerful anti-inflammatory diet designed to help individuals with autoimmune disease heal their gut, reduce flares, and restore immune tolerance.

The Ultimate Guide to the Paleo Autoimmune Protocol (AIP) Diet

Paleo Autoimmune Protocol (AIP) Diet: Heal Autoimmunity from the Inside Out

Autoimmune diseases affect over 50 million Americans, yet conventional medicine often stops at symptom suppression with immunosuppressants. But what if you could calm the immune system by removing the triggers that provoke it?

That’s the goal of the Paleo Autoimmune Protocol (AIP) diet—a comprehensive nutritional strategy designed to remove immune-reactive foods, heal the gut, and restore immune balance.

Whether you're dealing with Hashimoto’s thyroiditis, rheumatoid arthritis, psoriasis, lupus, or a mystery inflammatory condition, the AIP diet offers a root-cause, food-as-medicine approach to long-term healing.

What Is the Paleo Autoimmune Protocol (AIP) Diet?

The AIP diet is an elimination and reintroduction protocol rooted in the paleo diet. It’s designed to help people with autoimmune diseases identify trigger foods, reduce systemic inflammation, and heal gut barrier dysfunction, which is a core contributor to autoimmune disease.

It Builds on the Paleo Framework

Like the paleo diet, the AIP approach avoids:

  • Grains

  • Legumes

  • Dairy

  • Refined sugar

  • Processed foods

  • Industrial seed oils

But it goes further by also eliminating foods that, while technically “paleo,” can exacerbate autoimmunity, such as:

  • Eggs

  • Nightshade vegetables (tomatoes, peppers, eggplant, potatoes)

  • Nuts and seeds (including coffee and cocoa)

  • Alcohol

  • Emulsifiers, thickeners, and food additives

The Scientific Rationale Behind AIP

1. Leaky Gut (Intestinal Permeability)

Increased gut permeability allows partially digested food proteins, toxins, and microbes to enter the bloodstream—triggering an immune attack.

AIP removes foods that irritate the gut lining and supports the gut with nutrient-dense, anti-inflammatory foods like:

  • Bone broth (rich in glycine and glutamine)

  • Fermented vegetables (restores microbiome balance)

  • Organ meats (rich in vitamins A, D, E, and zinc)

2. Molecular Mimicry

Certain food proteins resemble human tissues. When the immune system reacts to a food protein, it may mistakenly attack your joints, thyroid, brain, or skin due to this similarity. Gluten, dairy, and nightshades are common culprits.

3. Microbiome Imbalance

Dysbiosis—a disruption in the microbial balance of the gut—can drive chronic inflammation and autoimmunity. AIP encourages probiotic-rich foods while avoiding sugar and processed carbs that feed pathogenic bacteria.

Phases of the AIP Diet

The AIP protocol has two major phases: elimination and reintroduction.

Phase 1: Elimination (30–90 days)

Remove all potential dietary triggers while emphasizing:

  • Nutrient-dense foods

  • Anti-inflammatory compounds

  • Gut-healing ingredients

Foods to Eliminate:

  • Grains (wheat, oats, corn, rice)

  • Legumes (beans, lentils, soy, peanuts)

  • Dairy

  • Nightshades (tomatoes, peppers, eggplant, white potatoes)

  • Eggs

  • Nuts and seeds (and their oils)

  • Alcohol

  • Coffee, chocolate (seeds)

  • NSAIDs (e.g., ibuprofen, aspirin)

  • Food additives (carrageenan, guar gum, xanthan gum)

Foods to Eat:

  • Grass-fed meats and wild-caught seafood

  • Organ meats (liver, heart)

  • Bone broth

  • Leafy greens and cruciferous vegetables

  • Sweet potatoes, winter squash

  • Fermented vegetables (sauerkraut, kimchi)

  • Coconut products (milk, oil, flour)

  • Fresh herbs and AIP-compliant spices (turmeric, ginger)

  • Healthy fats (olive oil, avocado, coconut oil)

Phase 2: Reintroduction (individualized)

Once symptoms improve significantly, begin reintroducing foods one at a time, spaced 5–7 days apart.

Steps for Reintroduction:

  1. Choose one food group (e.g., egg yolk).

  2. Eat a small amount in the morning.

  3. Monitor symptoms over 72 hours.

  4. If no reaction, reintroduce again in slightly larger amounts.

  5. If tolerated, include it in your diet.

Common reintroduction order (based on tolerance):

  1. Egg yolks

  2. Seeds and seed-based spices

  3. Nuts

  4. Nightshade fruits (e.g., tomatoes)

  5. Egg whites

  6. Grass-fed dairy (e.g., ghee, yogurt)

  7. White rice (for some people)

Who Should Try the AIP Diet?

You may benefit from the AIP diet if you have:

  • Hashimoto’s thyroiditis

  • Rheumatoid arthritis

  • Lupus (SLE)

  • Psoriasis

  • Multiple sclerosis

  • Celiac disease

  • Type 1 diabetes

  • Inflammatory bowel disease (Crohn’s or ulcerative colitis)

  • Sjögren’s syndrome

  • Eczema, asthma, or chronic urticaria

  • Post-viral or long COVID syndromes

  • Unexplained joint pain, fatigue, or brain fog

Clinical Research Supporting AIP

Several studies now support AIP’s role in reducing autoimmune symptoms:

1. IBD Symptom Reduction (2017)

A study published in Inflammatory Bowel Diseases evaluated 15 patients with Crohn’s disease or ulcerative colitis following the AIP diet. After 6 weeks:

  • 73% achieved clinical remission

  • Marked reductions in inflammation and symptom severity

2. Hashimoto’s Improvement (2019)

A pilot study on women with Hashimoto’s thyroiditis showed:

  • Significant reduction in fatigue and symptom scores

  • Improved quality of life

  • Decrease in TPO antibodies (thyroid autoimmunity marker)

3. Psoriasis Case Studies

Clinical reports document improved skin lesions and reduced need for biologic medications after adherence to AIP principles.

Benefits of the AIP Diet

Benefit Mechanism
Reduced Inflammation Eliminates immune triggers and gut irritants
Gut Healing Bone broth, fermented foods, and collagen support repair
Hormonal Balance Healthy fats and organ meats restore precursors
Brain Fog Reduction Anti-inflammatory fats support cognition
Autoantibody Reduction Removal of cross-reactive proteins (e.g., gluten)
Mitochondrial Support Nutrient density boosts energy production
Detoxification Liver support via greens, crucifers, and clean proteins

Functional Medicine Enhancements to AIP

To boost AIP results, functional medicine often includes:

🧬 Supplements

🔬 Peptide Support

  • BPC-157 – Enhances gut healing, immune modulation

  • KPV peptide – Inhibits NF-kB, reducing cytokine storms

  • TB-500 – Repairs tissue and modulates immune response

  • LL-37 – Antimicrobial defense for gut dysbiosis

Common Challenges on AIP (and How to Overcome Them)

Challenge Solution
Feeling restricted Focus on nutrient density and flavor; try new AIP recipes
Social dining stress Prepare ahead or bring compliant meals
Nutrient gaps Add organ meats and rotate vegetables
Detox symptoms Increase water, rest, and consider binders
Reintroduction anxiety Keep a food/symptom journal for clarity

Sample AIP Meal Plan (Day 1)

Breakfast:
Beef patties with sautéed spinach and sweet potatoes, side of fermented carrots

Lunch:
Wild-caught salmon over mixed greens with olive oil, roasted butternut squash

Snack:
Sliced cucumbers with guacamole, coconut yogurt (unsweetened)

Dinner:
Bison meatballs in bone broth sauce, steamed broccoli, mashed cauliflower

Final Thoughts

The Paleo Autoimmune Protocol is more than just a diet—it's a powerful healing framework. By eliminating immune triggers, rebuilding the gut, and restoring nutrient balance, AIP empowers people with autoimmunity to reverse symptoms naturally and regain vitality.

It’s not about being perfect—it’s about creating the right internal environment for your body to heal.

Ready to Begin Your AIP Journey?

At Revolution Health & Wellness, we guide patients through the AIP protocol with tailored meal planning, supplement support, peptide therapy, and lab testing to track results. If you’re tired of chasing symptoms, we’re here to help you heal at the root.

📞 Schedule a consultation today to start your personalized AIP plan.

References

  1. Konijeti GG, et al. (2017). Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease. Inflamm Bowel Dis.

  2. Abbott RD, et al. (2019). Effects of the Autoimmune Protocol Diet on Hashimoto’s Thyroiditis. Cureus.

  3. Vojdani A, Vojdani E, Kharrazian D. (2017). Reaction of Human Monoclonal Antibodies to Dietary Proteins in Autoimmunity. Nutrients.

  4. Fasano A. (2012). Leaky gut and autoimmune diseases. Clin Rev Allergy Immunol.

  5. Kresser C. (2019). The AIP Diet: What You Need to Know. ChrisKresser.com.