The AIP Nutrition Plan: Calm Autoimmunity and Heal the Gut
If you’re navigating the ups and downs of autoimmune disease, you’ve likely heard of the Autoimmune Paleo (AIP) diet—but what is it exactly, and why does it work?
In functional medicine, the AIP diet is more than a trend. It’s a therapeutic elimination diet designed to remove inflammatory triggers, support gut healing, and calm an overactive immune system.
In this post, we’ll dive into the what, why, and how of the AIP nutrition plan—and how it can support root-cause healing for autoimmune conditions.
What Is the AIP Diet?
The Autoimmune Protocol (AIP) is a science-based, short-term elimination diet that focuses on:
Removing common food triggers
Supporting gut lining repair
Rebalancing the immune response
Identifying food sensitivities through a structured reintroduction
It builds on the Paleo diet but goes further by removing additional immune-disrupting foods.
Why AIP Works for Autoimmunity: Functional Medicine Perspective
Autoimmune disease is often rooted in:
Leaky gut (intestinal permeability)
Chronic inflammation
Food sensitivities
Immune dysregulation
The AIP diet removes known irritants while focusing on nutrient-dense, healing foods that restore immune tolerance and reduce flares.
What You Eliminate on AIP (Phase 1)
Removed to lower immune burden and gut irritation:
Grains (including gluten-free)
Dairy
Legumes (including peanuts and soy)
Nightshades (tomatoes, peppers, eggplant, potatoes)
Eggs
Nuts and seeds (including seed-based spices)
Coffee and alcohol
Refined sugar and processed foods
Industrial seed oils (canola, soybean, corn)
What You Can Eat on AIP
Nutrient-dense, healing foods include:
Organic, grass-fed meats and wild-caught fish
Organ meats (liver, heart, kidney)
Cooked vegetables (non-nightshade)
Bone broth and collagen-rich soups
Fermented foods (if tolerated)
Healthy fats: olive oil, coconut oil, avocado
Herbs (basil, rosemary, thyme, ginger, turmeric)
The 4-Phase AIP Framework (Functional Medicine-Aligned)
1. Elimination Phase (30–90 days)
Remove all potential inflammatory triggers
Focus on gut healing, immune support, and symptom tracking
2. Maintenance Phase
Continue therapeutic foods while monitoring flare patterns and energy
3. Reintroduction Phase (one food at a time, 3–7 days apart)
Slowly reintroduce nutrient-dense foods (eggs, seeds, etc.)
Watch for reactions: fatigue, skin changes, joint pain, digestive upset
4. Personalization Phase
Customize your long-term nutrition plan based on tolerance, lifestyle, and labs
Sustain a diverse, whole-food diet that supports immune balance
Functional Medicine Tools to Pair with AIP
GI-MAP or stool testing – Assess gut health, infections, dysbiosis
Micronutrient panels – Identify deficiencies from long-standing leaky gut
Cortisol & stress testing – Address HPA axis dysfunction
Food sensitivity testing – Fine-tune your personalized food plan
Mind-body practices (HRV, breathwork) – Regulate immune system via nervous system pathways
Tips for AIP Success
Meal prep is key – Batch cook proteins, bone broth, and veggies
Work with a functional medicine provider to guide testing, reintroduction, and gut support
Be gentle with yourself—this is a journey of self-discovery and healing
Track symptoms in a food/mood journal to spot patterns
Real Results from AIP + Functional Medicine
Many clients report:
Reduced joint pain, skin issues, and fatigue
Better digestion and elimination
Improved mood and mental clarity
Fewer autoimmune flares
When combined with targeted testing, supplementation, and lifestyle support, AIP becomes a powerful tool in the functional medicine toolkit.
Conclusion: Food Is Information—Not Just Fuel
The AIP nutrition plan gives your immune system the space to rest, reset, and repair.
With the guidance of functional medicine, AIP can help you uncover food triggers, restore gut function, and reduce the inflammation driving autoimmune conditions.
Healing is possible—one bite at a time.
Our online “Gut Repair Program” is designed to guide you through healing your gut using AIP, supplements, and support tools.
Sign up to move into your healing journey!