Introduction
Autoimmune diet protocols are specialized eating plans designed to reduce inflammation, identify food sensitivities, and support gut health for individuals with autoimmune conditions. These conditions occur when the immune system mistakenly attacks healthy cells, tissues, and organs. Diet modification aims to reduce symptom flares, manage inflammation, and potentially slow disease progression by removing potential dietary triggers and focusing on nutrient-dense foods that support immune regulation and healing.
Different protocols share common foundations but vary in specific approaches, elimination phases, and reintroduction strategies. This cheatsheet provides an overview of the major autoimmune dietary approaches, their principles, and practical implementation strategies.
Core Principles of Autoimmune Diet Protocols
Foundational Concepts
- Gut Health Focus: All protocols emphasize improving intestinal barrier function (addressing “leaky gut”)
- Anti-Inflammatory Approach: Eliminating pro-inflammatory foods while incorporating anti-inflammatory nutrients
- Elimination and Reintroduction: Temporary removal of potential trigger foods followed by systematic reintroduction
- Nutrient Density: Emphasis on micronutrient-rich whole foods
- Personalization: Recognition that food sensitivities and optimal diet vary between individuals
- Lifestyle Integration: Acknowledging stress management, sleep, and exercise as essential companion strategies
Common Scientific Mechanisms
| Mechanism | Description | Dietary Approach |
|---|---|---|
| Gut Permeability Reduction | Decreasing intestinal barrier dysfunction | Remove irritants like gluten, processed foods, certain lectins |
| Microbiome Modulation | Supporting beneficial gut bacteria | Prebiotic fibers, fermented foods, diverse vegetables |
| Antigen Removal | Eliminating proteins that may trigger immune reactions | Avoiding common allergens (gluten, dairy, etc.) |
| Inflammatory Pathway Inhibition | Blocking activation of pro-inflammatory signals | Omega-3 fats, antioxidants, polyphenols |
| Immune System Support | Providing nutrients essential for immune regulation | Vitamin D, zinc, selenium, vitamin A |
| Tissue Repair Facilitation | Supporting healing of damaged tissues | Proteins, zinc, vitamin C, collagen precursors |
Major Autoimmune Diet Protocols
Comparison of Major Protocols
| Protocol | Key Features | Strictness Level | Best For | Developed By |
|---|---|---|---|---|
| Autoimmune Protocol (AIP) | Most comprehensive elimination diet | Very High | Multiple autoimmune conditions, unknown triggers | Dr. Sarah Ballantyne |
| Wahls Protocol | Emphasis on nutrient density and mitochondrial support | High | Multiple sclerosis, neurological conditions | Dr. Terry Wahls |
| GAPS Diet | Focus on gut healing through specific foods and stages | Very High | Neurological conditions, severe gut issues | Dr. Natasha Campbell-McBride |
| Specific Carbohydrate Diet (SCD) | Limits complex carbohydrates and focuses on monosaccharides | High | IBD, Crohn’s, ulcerative colitis | Dr. Sidney V. Haas/Elaine Gottschall |
| Low FODMAP | Restricts fermentable carbohydrates | Moderate | IBS, digestive symptoms | Monash University |
| Mediterranean AID | Combines AIP principles with Mediterranean diet focus | Moderate | Multiple autoimmune conditions with cardiovascular concerns | Various practitioners |
| Paleo Approach | Eliminates modern processed foods and agricultural products | Moderate | Milder autoimmune symptoms, preventative | Various practitioners |
| Gluten-Free | Eliminates only gluten-containing grains | Low | Celiac disease, gluten sensitivity | Medical standard |
Protocol-Specific Food Lists
Autoimmune Protocol (AIP) – Elimination Phase
Allowed Foods:
- All non-starchy vegetables (except nightshades)
- Starchy vegetables like sweet potatoes, cassava, plantains
- Fresh fruits (moderate amounts)
- Quality meats and seafood
- Bone broth and organ meats
- Coconut products
- Non-seed herbs
- Non-seed spices
- Vinegars (except grain-based)
- Honey and maple syrup (minimal amounts)
- Quality oils (olive, avocado, coconut)
Eliminated Foods:
- All grains and pseudo-grains
- All dairy products
- Eggs
- Nuts and seeds (including coffee)
- Nightshade vegetables (tomatoes, peppers, potatoes, eggplant)
- Legumes (including soy and peanuts)
- Processed vegetable oils
- Food additives and processed foods
- Alcohol
- NSAIDs
- Stevia and other non-nutritive sweeteners
Wahls Protocol (Level 3 – Wahls Paleo Plus)
Emphasized Foods:
- 9 cups of vegetables and fruits daily:
- 3 cups dark leafy greens
- 3 cups sulfur-rich vegetables
- 3 cups bright colored (no nightshades)
- Seaweed weekly
- Organ meats multiple times weekly
- Fish and seafood 3+ times weekly
- Bone broth daily
- Fermented foods daily
- Coconut oil and MCT oil
Eliminated Foods:
- Grains
- Dairy (except ghee)
- Eggs
- Legumes
- Nightshades
- Sugar
- Processed foods
Unique Features:
- Ketogenic approach with nutritional ketosis
- Intermittent fasting recommended
- Structured vegetable categorization
GAPS Diet (Full GAPS)
Emphasized Foods:
- Homemade meat stocks and bone broths
- Meats, poultry, fish
- Animal fats (tallow, lard)
- Eggs
- Fermented foods (homemade yogurt, kefir, sauerkraut)
- Vegetables (non-starchy)
- Fruits (limited)
- Nuts and seeds (properly prepared)
- Honey as primary sweetener
Eliminated Foods:
- All grains and pseudo-grains
- Starchy vegetables (potatoes, sweet potatoes)
- Milk (yogurt and kefir allowed)
- Sugar and artificial sweeteners
- Processed foods and additives
- Preservatives
Unique Features:
- Starts with Introduction Diet (6 stages)
- Heavy emphasis on probiotic foods
- Focuses on specific carbohydrate digestion
Specific Carbohydrate Diet (SCD)
Allowed Foods:
- Most unprocessed meats, poultry, fish
- Most vegetables
- Low-sugar fruits
- Properly fermented yogurt (homemade, 24-hour fermented)
- Hard cheeses
- Nuts and seeds
- Honey as the only sweetener
Eliminated Foods:
- All grains
- All sugars except honey
- Starchy vegetables (potatoes, sweet potatoes)
- Milk and soft cheeses
- Canned vegetables with additives
- Processed meats
- Most commercial products with additives
- Certain legumes
Unique Features:
- Focus on monosaccharides (simple sugars)
- Avoids disaccharides and polysaccharides
- Progressive introduction of allowed foods
Implementation Methodology
Step-by-Step Implementation Process
- Preparation Phase (1-2 weeks before starting)
- Research and choose the most appropriate protocol for your condition
- Stock kitchen with allowed foods and remove non-compliant items
- Meal plan and gather recipes
- Consider baseline testing (optional: inflammatory markers, gut health tests)
- Document current symptoms for baseline comparison
- Consult healthcare providers as needed
- Elimination Phase (30-90 days)
- Remove all restricted foods completely
- Focus on nutrient-dense alternatives
- Document symptoms, energy levels, and changes
- Address withdrawal symptoms and cravings
- Implement complementary lifestyle practices
- Ensure adequate caloric intake and nutrition
- Maintenance Period (variable)
- Continue strict protocol until symptomatic improvement plateaus
- Assess readiness for reintroductions
- Continue supportive lifestyle practices
- Reintroduction Phase (several months)
- Reintroduce single foods systematically
- Test each food for 3-7 days
- Document any reactions
- Wait for reactions to clear before next reintroduction
- Prioritize nutrient-dense foods and personal preferences
- Personalization Phase (ongoing)
- Establish your personalized dietary template
- Create sustainable long-term approach
- Continue monitoring symptoms
- Adjust as needed during flares
- Periodic reassessment with healthcare providers
Food Reintroduction Process
| Stage | Guidelines | Examples | Duration |
|---|---|---|---|
| Stage 1 | Most nutrient-dense, least likely to trigger | Egg yolks, seed spices, grass-fed ghee | 3-7 days per food |
| Stage 2 | Seeds and nuts, additional spices | Walnuts, chia seeds, cocoa, coffee | 3-7 days per food |
| Stage 3 | Higher quality dairy, eggs | Pastured egg whites, grass-fed butter | 3-7 days per food |
| Stage 4 | Nightshades, alcohol, additional foods | White potatoes, wine, legumes | 3-7 days per food |
| Stage 5 | Least recommended, rarely tolerated | Gluten, processed foods | Test with caution |
Reintroduction Protocol:
- Choose ONE food to reintroduce
- Start with small amount on day 1, increasing slightly on day 2-3 if no reaction
- Document all symptoms (digestive, skin, energy, pain, sleep, mood)
- If reaction occurs, remove food and wait until symptoms clear
- If no reaction, food can be included occasionally while continuing reintroductions
- Wait 3-7 days before introducing next food
Common Challenges and Solutions
Symptom Management During Transition
| Challenge | Description | Solution |
|---|---|---|
| Initial Flare | Temporary symptom increase when starting | Gradual transition, hydration, rest, gentle movement |
| Detox Symptoms | Headache, fatigue, irritability | Increase water, support liver with lemon water, gentle protocols |
| Carb Flu | Low energy from reduced carbohydrates | Increase starchy vegetables, ensure adequate calories |
| Constipation | Digestive slowdown | Increase water, add prebiotic fibers, magnesium supplementation |
| Hunger/Cravings | Unsatisfied or frequent hunger | Increase protein and healthy fats, address emotional aspects |
| Social Isolation | Difficulty eating out/with others | Preparation, communication, focus on inclusion not food |
| Food Boredom | Monotonous meals, recipe fatigue | Explore new recipes, spices, cooking methods |
| Orthorexia Risk | Unhealthy focus on “perfect” eating | Mindfulness, flexibility, focus on addition not restriction |
Nutritional Considerations
| Nutrient | Potential Deficiency Risk | Food Sources on Protocol | Supplement Considerations |
|---|---|---|---|
| Calcium | Moderate to High (dairy-free) | Bone broth, sardines, leafy greens | Cal-mag supplement if needed |
| Vitamin D | Variable (less sun exposure) | Fatty fish, liver, egg yolks | Testing and supplementation often needed |
| B Vitamins | Low to Moderate | Organ meats, nutritional yeast | B-complex if avoiding fortified foods |
| Iron | Low (if consuming meat) | Red meat, organ meats, shellfish | Monitor levels, supplement only if deficient |
| Fiber | Moderate (grain-free) | Vegetables, fruits, tiger nuts | Gradual increase in vegetable consumption |
| Magnesium | Moderate | Leafy greens, avocado | Often beneficial as supplement |
| Iodine | Moderate | Seaweed, fish | Consider supplementation if avoiding iodized salt |
| Vitamin K2 | Low | Fermented foods, grass-fed meats | Often paired with vitamin D supplements |
Best Practices and Tips
Meal Planning Strategies
- Batch cook proteins and vegetables 2-3 times weekly
- Use one-pan meals for simplicity
- Employ freezer meals for backup options
- Create a rotating meal framework rather than strict meal plan
- Use theme nights (stir-fry, soup, sheet pan meals)
- Prep components rather than full meals for flexibility
- Keep emergency compliant snacks accessible
- Plan for leftovers to minimize cooking frequency
Kitchen Time-Saving Tips
- Invest in time-saving equipment (Instant Pot, slow cooker)
- Pre-chop vegetables for quick assembly
- Make sauces and dressings in batches
- Use appropriate storage containers for pre-prepped items
- Organize refrigerator with protocol foods easily visible
- Keep a well-stocked freezer with protocol-compliant options
- Maintain a spice drawer with allowed seasonings
- Create flavor profiles with herb/spice combinations
Eating Out and Socializing
- Research menu options in advance
- Call restaurants to discuss dietary needs
- Choose simple preparations (grilled proteins, steamed vegetables)
- Bring your own dressings/sauces when possible
- Consider eating before social events
- Offer to bring a compliant dish to gatherings
- Focus on the social aspect rather than the food
- Practice clear, non-apologetic communication about needs
Lifestyle Integration for Maximum Benefit
- Prioritize stress management (meditation, nature, mindfulness)
- Ensure adequate sleep (7-9 hours in dark environment)
- Incorporate gentle movement daily
- Practice mindful eating
- Maintain food-symptom journal
- Sunlight exposure for vitamin D and circadian rhythm
- Reduce environmental toxin exposure
- Build a supportive community (in-person or online)
Resources for Further Learning
Recommended Books by Protocol
- AIP: “The Autoimmune Protocol” by Sarah Ballantyne, PhD
- Wahls Protocol: “The Wahls Protocol” by Terry Wahls, MD
- GAPS: “Gut and Psychology Syndrome” by Dr. Natasha Campbell-McBride
- SCD: “Breaking the Vicious Cycle” by Elaine Gottschall
- Multiple Approaches: “The Autoimmune Solution” by Amy Myers, MD
Helpful Websites and Apps
- AutoimmuneWellness.com
- ThePaleoMom.com
- WahlsProtocol.com
- SCDLifestyle.com
- AIPRecipeCollection.com
- Monash University FODMAP App
- Real Plans (meal planning app with AIP/Paleo options)
- ChronoMeter (nutrition tracking)
Scientific Research Resources
- PubMed.gov for peer-reviewed studies
- The Paleo Approach Sciencey Blog
- Autoimmune Institute Research Database
- Wahls Research Papers (University of Iowa)
- American Autoimmune Related Diseases Association
Finding Professional Support
- Functional Medicine Practitioners Directory (IFM.org)
- AIP Certified Coaches
- Registered Dietitians with autoimmune specialization
- Integrative Medical Doctors
- Online support programs and group coaching
Important Note: This cheatsheet is for informational purposes only and is not medical advice. Always consult with qualified healthcare providers before making significant dietary changes, especially if you have an autoimmune condition or other health concerns. Different autoimmune conditions may respond differently to various protocols, and individual needs vary widely.