Should I Do Low FODMAP or AIP?: A Guide to Choosing the Right Diet

October 16, 2025 •

6 min read

Estimates suggest that Irritable Bowel Syndrome (IBS) affects up to 12% of the population, while autoimmune diseases affect millions. To manage chronic symptoms, many turn to elimination diets, often debating, "Should I do low fodmap or AIP?".

Quick Summary

Choosing between the Low FODMAP and AIP diet depends on your primary health concerns. The Low FODMAP diet targets IBS and gut symptoms, while AIP addresses autoimmune conditions and inflammation. Both are short-term elimination protocols aimed at identifying personal food triggers through a structured process.

Key Points

Primary Goal: The Low FODMAP diet targets digestive issues like Irritable Bowel Syndrome (IBS), while the AIP diet focuses on systemic autoimmune inflammation.
Dietary Restriction: The AIP diet is typically more restrictive, eliminating entire food groups like eggs, nuts, and nightshades, whereas Low FODMAP targets specific fermentable carbohydrates.
Duration: Both are short-term elimination diets, not permanent lifestyles. The elimination phase can last from 2-6 weeks for Low FODMAP and 30-90 days for AIP.
Professional Guidance: It is critical to work with a dietitian or healthcare provider for either diet to navigate restrictions, identify triggers, and avoid nutritional deficiencies.
Choosing the Right One: Base your choice on your primary symptoms and a medical diagnosis. Focus on gut-related issues for Low FODMAP, and autoimmune concerns for AIP.
Reintroduction is Key: A structured reintroduction phase is essential for both diets to identify personal trigger foods and expand your dietary variety long-term.

Navigating the world of therapeutic diets can be overwhelming, especially when faced with complex options like the Low FODMAP diet and the Autoimmune Protocol (AIP) diet. While both are effective elimination diets that focus on whole foods and identifying trigger foods, they target different underlying health issues. Understanding their distinct approaches is crucial for anyone wondering which path is right for them.

The Low FODMAP Diet Explained

The Low FODMAP diet was developed by researchers at Monash University to manage symptoms of Irritable Bowel Syndrome (IBS) and other functional gastrointestinal disorders. The acronym FODMAP stands for Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols. These are short-chain carbohydrates that can be poorly absorbed in the small intestine. When they reach the large intestine, gut bacteria ferment them, which can lead to gas, bloating, and pain in people with sensitive digestive systems.

The diet consists of three phases:

Elimination Phase: For 2 to 6 weeks, all high-FODMAP foods are removed to give the digestive system a rest. Relief can be significant, with studies showing effectiveness in up to 75% of IBS cases.
Reintroduction Phase: Different FODMAP groups are systematically reintroduced one at a time to identify which specific types and amounts cause symptoms.
Personalization Phase: Based on your findings, you create a long-term diet that minimizes only your personal trigger FODMAPs, allowing for the maximum dietary diversity you can tolerate.

Who is the Low FODMAP diet for?

This diet is primarily for those with a medical diagnosis of IBS or Small Intestinal Bacterial Overgrowth (SIBO) who experience symptoms like bloating, gas, abdominal pain, diarrhea, and constipation. It is not a permanent diet and should be undertaken with supervision from a qualified dietitian to ensure nutritional needs are met.

The Autoimmune Protocol (AIP) Diet Explained

The AIP diet is a more extensive elimination protocol designed to reduce inflammation and support the immune system in individuals with autoimmune conditions. The protocol is based on the theory that a "leaky gut"—or increased intestinal permeability—contributes to autoimmune responses by allowing foreign particles to enter the bloodstream. AIP aims to heal the gut lining by removing potential inflammatory triggers.

The AIP diet's elimination phase is highly restrictive and typically lasts longer, around 30 to 90 days, or until symptoms noticeably improve.

Key foods eliminated in the AIP diet include:

Grains (all types)
Legumes (beans, lentils, peanuts)
Dairy
Eggs
Nuts and seeds
Nightshade vegetables (tomatoes, potatoes, peppers, eggplant)
Refined sugars and processed foods
Alcohol and coffee

The diet is rich in nutrient-dense whole foods like fresh vegetables (non-nightshade), fruit, high-quality meats, organ meats, and fermented foods. Like Low FODMAP, it has a reintroduction phase to test individual tolerances, followed by a maintenance phase. Early research in conditions like inflammatory bowel disease (IBD) and Hashimoto's thyroiditis has shown promising results in improving quality of life and reducing symptoms.

Who is the AIP diet for?

This protocol is designed for individuals with diagnosed autoimmune diseases such as lupus, rheumatoid arthritis, IBD, and Hashimoto's. It is also highly restrictive and should be done under medical guidance, especially for those with a history of eating disorders or nutritional deficiencies.

Low FODMAP vs. AIP: A Comparison


Feature	Low FODMAP Diet	AIP Diet
Primary Target	Functional digestive disorders like IBS and SIBO.	Autoimmune diseases and systemic inflammation.
Mechanism	Reduces fermentation of specific carbohydrates in the gut.	Heals the gut lining by eliminating potential inflammatory triggers.
Level of Restriction	Moderate. Focuses on fermentable carbohydrates; some food types are allowed in small quantities.	High. Eliminates entire food groups like grains, dairy, eggs, nuts, and nightshades.
Elimination Phase	2–6 weeks.	30–90 days or until symptoms improve.
Key Eliminated Foods	High-FODMAP foods like onions, garlic, wheat, certain fruits, and dairy.	Grains, legumes, dairy, eggs, nuts, seeds, nightshades.
Key Recommended Foods	Low-FODMAP vegetables, fruits, proteins, and grains (e.g., rice, quinoa).	Nutrient-dense vegetables (non-nightshade), meats, fish, bone broth, and fermented foods.
Duration	Short-term elimination with personalized long-term plan.	Initial elimination followed by potentially longer-term maintenance.

How to Choose the Right Diet for You

The decision of whether to pursue Low FODMAP or AIP should be based on your primary health concerns, symptom patterns, and consultation with a healthcare professional, like a registered dietitian.

Prioritize Your Primary Symptoms

For digestive symptoms: If your main complaints are IBS-like symptoms such as bloating, gas, and abdominal pain without a known autoimmune diagnosis, the Low FODMAP diet is the more direct and less restrictive path to explore first. Studies show it is highly effective for these issues.
For systemic inflammation: If you have a diagnosed autoimmune disease and experience widespread inflammation, joint pain, fatigue, or skin issues, the AIP diet is designed to target these systemic immune responses. Its broader elimination approach may uncover triggers that a Low FODMAP diet would miss.

Consider the Potential Risks

Both diets carry risks, primarily due to their restrictive nature:

Nutrient Deficiencies: Eliminating entire food groups can lead to deficiencies in important nutrients like fiber, calcium, and magnesium. Professional guidance is crucial to prevent this.
Gut Microbiome Changes: Long-term restriction of prebiotics found in many FODMAP foods can negatively impact the diversity of your gut bacteria.
Disordered Eating: The restrictive nature of these diets, particularly AIP, can create food anxiety and orthorexia in vulnerable individuals.

Working with a Professional

Given the complexity and restrictive nature of these protocols, attempting either one without professional support is not recommended. A dietitian can help you:

Ensure you are meeting your nutritional needs throughout the process.
Accurately implement the elimination and reintroduction phases.
Interpret your symptoms and tolerance levels correctly.
Navigate potential overlaps, such as when IBD patients have concurrent IBS symptoms.

Conclusion

Ultimately, there is no single right answer to the question, "Should I do low fodmap or AIP?" The choice depends entirely on your specific health condition and primary symptoms. The Low FODMAP diet is a scientifically validated approach for managing IBS, targeting fermentable carbohydrates. The AIP diet is a more intensive protocol aimed at reducing systemic inflammation in autoimmune diseases by healing the gut. Both are powerful, but restrictive, short-term tools, not long-term lifestyle diets. Crucially, both require a structured, phased approach under the supervision of a healthcare professional to identify individual triggers safely, restore gut health, and expand dietary variety over time.

For up-to-date guidance on the Low FODMAP diet, resources like the Monash University FODMAP App are invaluable. To explore more about the AIP approach and personal recovery stories, resources like Autoimmune Wellness can provide insight. A thoughtful, guided approach is the key to successful symptom management and improved quality of life.

The Reintroduction Phase: Your Long-Term Plan

One of the most important aspects of either the Low FODMAP or AIP diet is the reintroduction phase, which is often challenging for people to navigate. Many become hesitant to reintroduce foods after experiencing symptom relief, but this can lead to nutrient deficiencies and unnecessary long-term restriction. Here's how to make it work:

Introduce one food group at a time: Focus on testing one new food item or FODMAP group every 5-7 days.
Monitor symptoms carefully: Keep a detailed food and symptom diary to track your body's response to each food introduction.
Use a controlled approach: Start with a small amount, wait for a reaction, and if none occurs, increase the portion size.
Listen to your body: If symptoms return, that food group may be a trigger for you. Avoid it for a while and re-test later, as tolerance can change over time.
Expand your food freedom: The goal is to eat the widest variety of foods possible without triggering symptoms. This helps ensure you get a broad range of nutrients and improves your overall quality of life.

Ultimately, the reintroduction phase transforms these restrictive protocols into personalized, sustainable eating plans.

Frequently Asked Questions

While it's possible to combine elements of both diets, it is highly restrictive and challenging to do. Most experts recommend starting with one protocol based on your primary symptoms and adding or adjusting later, but only under the guidance of a healthcare professional.

Your choice should be based on your primary health issue and symptoms. If your main problems are digestive (bloating, gas, pain) and you have an IBS or SIBO diagnosis, Low FODMAP is the most targeted approach. If you have a diagnosed autoimmune condition and experience chronic inflammation, the broader approach of AIP is more appropriate.

FODMAP is an acronym for Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols. These are short-chain carbohydrates found in many foods that can be poorly absorbed and fermented in the gut, causing digestive symptoms in sensitive individuals.

Anyone with a history of eating disorders or at risk for malnutrition should generally avoid these restrictive diets unless under strict medical supervision. Additionally, individuals without a diagnosed condition targeted by the diet should not follow it.

If you don't experience a noticeable improvement in symptoms during the elimination phase (typically 2-6 weeks for Low FODMAP, 30-90 days for AIP), it may indicate that food triggers are not the primary cause of your symptoms, or that the specific diet is not the right fit for you. In this case, you should consult with your doctor to explore other diagnostic and treatment options.

The Low FODMAP elimination phase is typically 2 to 6 weeks. The AIP elimination phase can last from 30 to 90 days, or until significant symptom reduction is achieved.

The reintroduction phase is the systematic process of adding eliminated foods back into your diet, one at a time. The purpose is to determine which foods you can tolerate and which ones trigger your symptoms, allowing for a personalized, long-term eating plan.

The AIP diet is based on the principles of the Paleo diet but is significantly stricter. While Paleo eliminates grains, legumes, and dairy, AIP further removes potential immune-triggering foods like eggs, nuts, seeds, and nightshade vegetables.