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Written by
Michelle Darian
Medically Reviewed by
Dr. Anshul Gupta

Because your body’s immune system is responsible for protecting you from harm, when it detects something that shouldn’t be there — for example, pathogenic bacteria or viruses — an immune response is initiated. Protective mechanisms are recruited to localize and remove the threat from the body. In the case of bacteria or viruses, the immune response is a healing process. (Source)

However, there are conditions in which the immune system goes into overdrive and targets healthy cells with these otherwise protective measures. These conditions are referred to as autoimmune diseases. While nutrition and lifestyle factors alone don’t reverse autoimmune diseases, they can be powerful tools in lowering inflammation and reducing symptoms. Read on to learn more about the AIP diet and the nine foods to avoid with autoimmune diseases. (Source)

What Is the Autoimmune Protocol (AIP) Diet? 

The AIP diet was developed for patients with autoimmune conditions to help determine if certain types of food were increasing their body's inflammation levels. The AIP dietary approach to autoimmune symptom reduction is by healing the gut and replenishing nutrient stores to nourish the immune system. Interestingly, healing the gut has been shown to reduce autoimmune-related inflammation. (Source

The first phase of the AIP diet is the elimination phase, in which specific types of foods known to cause sensitivities and intolerances are removed from the diet. At the same time, nutrient-dense foods that support healing are added in. As symptoms subside, the reintroduction phase begins. Here, foods are slowly reintroduced while carefully monitoring for reactions. Inflammatory bowel disease, lupus, and rheumatoid arthritis are examples of autoimmune diseases for which the AIP diet may be recommended. (Source

spoonfuls of grains, foods to avoid with autoimmune diseases

Foods to Avoid on the Autoimmune Protocol

The foods eliminated during the first phase of the AIP diet were selected for a few reasons — they are either pro-inflammatory, are common allergens, or contain compounds that either impair the gut lining or increase the diversity of bad gut bacteria. The elimination phase is temporary, and typically lasts between 30 and 90 days. The length of the elimination phase is tailored to each person, depending on their specific symptoms and condition severity. (Source

Here are the nine foods to avoid on the AIP diet, with an explanation and a recommendation of alternatives.


Legumes contain the plant compound lectin. Lectins can potentially impair the gut lining by increasing intestinal permeability — meaning substances, including those that are harmful like bacteria, can pass more freely out of the gut. Due to their impact on the gut microbiome, which plays an important role in inflammation, legumes like beans, lentils, and peas should be avoided when following the AIP diet. (Source)


Avoid grains like rice, wheat, barley, and bulgur for the same reasons that legumes are to be avoided on the AIP diet. Grains also contain the plant compound lectin, which can impair the gut lining and the gut flora, putting it into a pro-inflammatory state. (Source

Nightshade Vegetables

Nightshade vegetables, like legumes, are also rich in lectins that can exacerbate leaky gut symptoms by increasing intestinal permeability. This is problematic because it increases the risk of bacteria and toxins making their way out of the gut. Examples of nightshade vegetables include eggplant, tomatoes, peppers, and tomatoes. (Source

Eggs and Dairy

Eggs and dairy contain dietary cholesterol and saturated fats. Consuming foods rich in both cholesterol and saturated fat are associated with increased inflammation levels in the body. In addition, cow’s milk and eggs are among the top eight most common allergens, making them foods to avoid on the AIP diet. (Source, Source)

Red Meats: Higher in Saturated Fats 

Certain red meats, specifically those higher in saturated fat, are associated with increased inflammation levels. Saturated fat intake is associated with increased pro-inflammatory cytokine production. Because cytokines are small proteins that control the activity of immune cells, this means that saturated fat can increase inflammation levels. And, higher amounts of total meat intake are associated with increased inflammation levels. 

However, the AIP diet does not write off red meat altogether — the quality of the red meat matters. Meat from animals fed a diet of grass throughout their lifespan is higher in omega-3 fatty acids and lower in omega-6 fatty acids, a beneficial ratio for inflammation levels. This is because grass diets are higher in phytonutrients than grain diets, resulting in meat that is high in beneficial fatty acids and antioxidants. Selecting the right red meats and organ meats can help restore vital nutrients. (Source, Source

Added Sugars, Refined Sugars, Non-Nutritive Sweeteners, and Sugar Alcohols

When sugars are refined, they lose their fiber and other nutritional value. Without fiber to slow them down, refined sugars enter the bloodstream more quickly, leading to blood glucose spikes. Over time, frequent blood sugar spikes are associated with higher inflammation levels. Conversely, fiber, a nutrient lost during processing, helps to slow the absorption of foods into the bloodstream, reducing blood sugar spikes. This helps keep you fuller for longer, and is also associated with reduced inflammation levels. Therefore refined sugars, including both white and brown sugar, should be avoided in the AIP diet. (Read our comprehensive review of two commonly used artificial sweeteners.) (Source)

Nuts and Seeds

Nuts and seeds are among the top most common food allergens. Because nuts and seeds have a symptomatic allergy-producing effect on a sizable portion of the population, it’s recommended that all nuts and seeds be avoided during the elimination phase of the AIP diet. Spices that derive from seeds, like mustard, nutmeg, and pepper, should also be avoided during this phase of the AIP diet. (Source, Source

Refined Oils and Seed Oils 

Similar to nuts and seeds, seed oils such as canola, sunflower, and soybean should also be avoided in the AIP diet to reduce inflammatory exposures.. And similar to refined sugars, highly refined oils such as canola oil should be removed during the elimination phase of the AIP diet, and potentially beyond due to its inflammatory properties . (Source, Source

Certain Beverages: Alcohol and Coffee

Beverages such as alcohol and coffee should be eliminated in the AIP diet. Alcohol can increase the permeability of the gut lining, weakening it and allowing particles such as pathogens to pass through it more easily. Consuming alcohol is also associated with a higher abundance of bad gut bacteria, which have a pro-inflammatory effect. (Source)

While coffee is rich in dietary polyphenols, which can produce anti-inflammatory effects, coffee is to be avoided on the AIP. The reasoning for temporarily skipping your morning cup of coffee during the elimination phase of AIP is to reduce inflammation and potential food intolerance symptoms. Here are nine anti-inflammatory beverages to include instead. (Source, Source)

bowl of greens

Foods to Include on the Autoimmune Protocol

Plant Fats

When following the AIP diet, aim to include minimally processed plant-based fats such as extra virgin olive oil, avocados, and avocado oil. Two components of extra virgin olive oil contribute to its beneficial impacts on the body: monounsaturated fatty acids and polyphenols. Monounsaturated fats help to increase HDL cholesterol (the “good” cholesterol), which is responsible for scavenging and removing LDL cholesterol (the “bad” cholesterol) from the body. Optimal HDL and LDL cholesterol levels are associated with healthy arteries and cells. The polyphenolic content of olive oil can also directly impact inflammation levels by reducing cytokine production. (Source

Animal Fats

Choose grass-fed, lean meats. Lean meat tends to be lower in saturated fat, and saturated fat can trigger a pro-inflammatory response. Grass-fed beef also contains vitamins and antioxidants that help reduce inflammation. Bone broth and organ meats are nutrient-dense foods to include on the AIP diet. (Source

Fish and shellfish are also foods to include on the AIP diet. Bass, catfish, cod, clams, and crab are vitamin-rich options. (Source


When following the AIP diet, include plenty of cruciferous and non-starchy vegetables such as broccoli, cauliflower, asparagus, garlic, leeks, and cucumbers. These vegetables contain many anti-inflammatory vitamins, minerals, and antioxidants while limiting gut reactivity. (Source)


Fruits such as berries, melons, citrus, and tropical fruits are excellent foods to include on the AIP diet. Berries are particularly rich in anti-inflammatory dietary polyphenols. Fruits are also rich in fiber, an important nutrient when it comes to the gut. Fiber increases the abundance and diversity of “good” gut bacteria. (Source)

Our ultimate AIP food list is a comprehensive overview of foods to include while following the AIP diet. 

How Does the AIP Diet Work?

The Elimination Phase

The elimination phase is the first phase of the AIP diet. During the elimination phase, the foods listed above are removed from the diet for a specific time period. The foods removed are either allergy-producing, pro-inflammatory, or impair gut permeability. Along with eliminating particular foods, nutrient dense foods are strategically added. This phase typically lasts between 30 and 90 days in duration, depending on each individual’s symptoms. The reasoning for this is to allow the body ample time to recover from an extended time of inflammatory food consumption while repleting necessary nutrients. (Source

The Reintroduction Phase

The reintroduction phase is a step-by-step reintroduction of foods, which are slowly added back into the diet one by one. Symptoms are monitored closely during the reintroduction phase. Foods that produce symptoms should continue to be eliminated. After approximately one week of monitoring for symptoms, the next food can be reintroduced, and so on. To learn more about getting started with the AIP diet, check out this guide. (Source

The Personalization Phase 

After foods have been reintroduced and you’ve identified what food staples trigger your unique autoimmune symptoms, you can use this insight to inform how to personalize your diet. Because autoimmunity is experienced differently for everyone, no two personalized diets will look the same. This personalized diet can then be implemented long-term to help avoid intestinal inflammation and uncomfortable autoimmune flare-ups. (Source

papaya and citrus fruits

What Are the Benefits of Following the AIP Diet? 

Heal a Leaky Gut

Leaky gut is a condition in which the intestinal lining has increased permeability, allowing more toxins and bacteria to “leak” into the bloodstream. Leaky gut may contribute to the symptoms of autoimmune diseases. While there is no current treatment for leaky gut, adhering to the principles of the AIP diet has the potential to help. (Source

Reduced Inflammation and Symptoms of Some Autoimmune Disorders

Similar to leaky gut, chronic inflammation doesn’t have a specific cure; rather, eliminating pro-inflammatory foods can help to reduce inflammation levels in the body. Treatment for many autoimmune conditions (e.g., inflammatory bowel disease) relies on reducing pro-inflammatory foods and increasing anti-inflammatory foods. (Source)

The Bottom Line on Foods to Avoid with Autoimmune Diseases

The major foods to avoid with autoimmune diseases include legumes, grains, nightshade vegetables, eggs, dairy, red meats, added sugar, nuts and seeds, refined oils and seed oils, and beverages such as coffee and alcohol. This particular nutritional approach is known as the autoimmune protocol (AIP) diet. 

When following the AIP diet, it’s important to eliminate foods most associated with producing or exacerbating autoimmune disease symptoms while simultaneously including nutrient-dense, anti-inflammatory foods that strengthen good gut bacteria. 

The WellTheory membership can help take the guesswork out of adhering to the AIP diet. Working with a Nutritional Therapy Practitioner can provide hands-on guidance during the elimination phase of the diet, and help you strategically reintroduce foods when the time is right. 

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9 Foods to Avoid on the Autoimmune Protocol With Autoimmune Diseases

You know your diet affects your health. Learn how to reduce symptoms and feel better by knowing which foods to avoid with autoimmune diseases.
Medically Reviwed
Written by
Michelle Darian
Medically Reviewed by
Dr. Anshul Gupta
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