What is the best protein for autoimmune disease? A comprehensive guide

October 5, 2025 •

4 min read

According to the American Autoimmune Related Diseases Association, up to 50 million Americans suffer from autoimmune diseases. For many of these individuals, diet, and specifically the right protein, can play a significant role in managing symptoms. Finding the right protein for an autoimmune disease is a personalized journey that prioritizes reducing inflammation and supporting gut health.

Quick Summary

This guide examines optimal protein sources for managing autoimmune disease, focusing on gut-repairing options like collagen, anti-inflammatory fish and plant proteins, and identifying common dietary triggers. It details how to select high-quality protein powders and customize your diet for better health.

Key Points

Prioritize Gut Healing: Focus on proteins like collagen peptides and bone broth, which contain amino acids crucial for repairing a compromised intestinal lining.
Choose Anti-Inflammatory Options: Incorporate wild-caught fatty fish, hemp protein, and grass-fed beef for their anti-inflammatory properties and omega-3 content.
Identify Individual Triggers: Recognize and test for sensitivities to common trigger proteins, such as dairy (casein, whey), eggs, gluten, and legumes, which can cause inflammation.
Opt for Clean Protein Powders: When using supplements, choose high-quality, pure options like hydrolyzed beef protein or hemp protein, avoiding artificial additives and fillers.
Follow an Elimination Protocol: A structured elimination diet, like the Autoimmune Protocol (AIP), can help systematically identify specific protein and food intolerances.
Embrace a Whole Foods Diet: The best protein choice is part of a larger anti-inflammatory diet rich in whole, unprocessed fruits, vegetables, and healthy fats.

The link between diet, gut health, and autoimmune diseases is a critical area of functional medicine, with research showing that a compromised gut lining, often referred to as 'leaky gut,' can drive systemic inflammation. For individuals with autoimmune conditions, choosing the right protein is not just about muscle repair but about selecting amino acids that can help heal the gut, modulate the immune system, and reduce inflammation.

The Crucial Role of Protein in Autoimmune Support

Protein is vital for tissue repair and immune function. In autoimmune diseases, where the body's immune system attacks its own tissues, providing the right building blocks is essential for the body to heal and regulate itself. The gut, which houses a large portion of the immune system, is particularly sensitive to dietary proteins. Certain amino acids are fundamental to this process:

Glutamine: This amino acid is a primary fuel source for the cells lining the intestines, called enterocytes. It is crucial for maintaining the integrity of the intestinal lining, preventing unwanted substances from entering the bloodstream and triggering an immune response.
Glycine and Proline: Found abundantly in collagen and bone broth, these amino acids are integral to repairing and strengthening the gut lining.

Top Protein Sources for an Anti-Inflammatory Diet

Not all protein is created equal when it comes to managing an autoimmune condition. Focusing on minimally processed, high-quality, and nutrient-dense sources is key to minimizing inflammation and maximizing benefits.

Animal-Based Proteins

Bone Broth & Collagen Peptides: Excellent for gut health and joint support, collagen peptides and bone broth are rich in gut-healing amino acids like glycine and glutamine. They are particularly beneficial for those with compromised gut barriers or joint pain. Sourcing grass-fed options is recommended for higher quality.
Wild-Caught Fatty Fish: Rich in anti-inflammatory omega-3 fatty acids, fish like salmon, sardines, and mackerel can help modulate immune activity and reduce inflammation.
Grass-Fed Beef and Pastured Poultry: These provide a full amino acid profile and are generally lower in inflammatory saturated fats compared to their conventionally raised counterparts. They are also encouraged on diets like the Autoimmune Protocol (AIP).

Plant-Based Proteins

For those who tolerate them, certain plant proteins offer significant anti-inflammatory benefits and other nutrients.

Hemp Protein: An anti-inflammatory, plant-based option rich in fiber and omega-3s, hemp protein is a versatile choice for vegan and vegetarian diets.
Pumpkin Seed Protein: High in zinc, magnesium, and antioxidants, pumpkin seed protein can support thyroid and immune function, making it an excellent choice for those with thyroid-related autoimmune issues like Hashimoto's.
Quinoa: A complete protein source, quinoa can be a good option if tolerated. However, some individuals with severe gut issues might find it irritating.

Comparison of Common Protein Sources for Autoimmunity


Protein Source	Gut-Healing Benefits	Anti-Inflammatory Properties	Common Trigger Concerns	Elimination Diet Compatibility (e.g., AIP)
Collagen/Bone Broth	High. Rich in glycine, proline, glutamine to repair gut lining.	Often anti-inflammatory.	Very low. Generally well-tolerated.	Yes, high compatibility.
Wild-Caught Fish	Supportive, via omega-3s for inflammation.	High. Rich in omega-3s.	Low. Generally safe, but test individual tolerance.	Yes, compatible.
Hemp Protein	Supportive, via fiber and amino acids.	High. Anti-inflammatory profile.	Low. Plant-based and generally safe.	Yes, compatible.
Grass-Fed Beef	Supportive, providing essential amino acids.	Moderate. Better than conventional beef.	Low. Ensure grass-fed and lean cuts.	Yes, compatible.
Pea Protein	Mixed. Can be anti-inflammatory, but may cause digestive upset in some.	Moderate.	Moderate. As a legume, it can trigger symptoms in sensitive individuals.	No, not in the initial phase.
Whey Protein	Can be inflammatory for those with dairy sensitivity.	Mixed. Can boost antioxidants, but casein can be problematic.	High. Casein and lactose can trigger flare-ups.	No, not compatible.
Soy Protein	Mixed. Can be problematic for some gut issues.	Mixed. May interfere with thyroid function.	High. A common allergen that can cause issues.	No, not compatible.

Choosing the Right Protein Powder

When opting for a supplement, the quality and purity are paramount. Read ingredient labels carefully to avoid artificial sweeteners, fillers, and additives that can exacerbate inflammation.

Collagen Peptides: Sourced from grass-fed animals and hydrolyzed for better absorption, these are a top choice for gut and joint health.
Hydrolyzed Beef Protein: Derived from grass-fed beef, this is a clean, AIP-compliant option that supports gut integrity.
Plant-Based Options: For those who prefer or require plant-based proteins, hemp or pumpkin seed protein are excellent choices. Ensure they are free of additives. Some people can tolerate pea protein, but it requires careful testing.

Identifying and Avoiding Inflammatory Triggers

For many with autoimmune conditions, certain proteins can act as triggers, causing inflammation and flare-ups. Elimination diets, like the Autoimmune Protocol (AIP), are designed to identify these sensitivities. Common triggers include:

Dairy: The casein and whey proteins in dairy products can cause significant inflammation for some individuals.
Gluten: Found in wheat, barley, and rye, gluten can increase intestinal permeability, contributing to the autoimmune response.
Eggs: The protein lysozyme in eggs can be difficult to break down for individuals with a compromised gut, triggering an immune reaction.
Legumes: Contain lectins, which can impair the gut lining and trigger inflammation.

The Personalized Approach to Protein

Ultimately, the best protein for autoimmune disease is not a one-size-fits-all solution. It requires a personalized, elimination-based approach to identify what your body tolerates best. The journey often involves starting with well-tolerated, gut-healing options and carefully reintroducing potential triggers while monitoring symptoms. Combining a nutrient-dense, anti-inflammatory diet with a high-quality protein source that works for your unique body can provide significant support. For guidance on this process, consider consulting a healthcare provider with expertise in functional medicine.

An anti-inflammatory eating style like the Mediterranean diet, which emphasizes whole foods, healthy fats, and fish, can be highly effective in reducing overall inflammation. You can learn more about its principles from authoritative sources like the Cleveland Clinic.

Frequently Asked Questions

Protein is essential for tissue repair and immune function. For those with autoimmune conditions, choosing proteins rich in specific amino acids like glutamine and glycine can help repair the gut lining and regulate the immune system, reducing overall inflammation.

Yes. Collagen and bone broth are rich in amino acids like glycine and proline, which are essential for healing and strengthening the intestinal lining. They are often recommended for those experiencing gut permeability, also known as 'leaky gut,' which is linked to autoimmunity.

Dairy proteins, specifically casein and whey, can be inflammatory triggers for many individuals with autoimmune diseases. Casein, in particular, has a chemical structure that can resemble body tissues, potentially confusing the immune system and causing it to increase its attacks.

Yes, many plant-based proteins are excellent choices. Hemp and pumpkin seed proteins are often well-tolerated and provide anti-inflammatory benefits. For those who can tolerate legumes, properly prepared pea protein or quinoa can also be good options, as they offer a complete amino acid profile.

When selecting a protein powder, prioritize options that are minimally processed and free of common allergens and inflammatory additives. Good choices include hydrolyzed beef protein, collagen peptides from grass-fed sources, and pure hemp protein. Always check labels for artificial sweeteners, fillers, and preservatives.

The AIP diet is an elimination diet designed to identify food triggers for autoimmune flares. It involves removing potentially inflammatory foods, including some common protein sources like dairy, eggs, nuts, and legumes, for a period. It then reintroduces them slowly to determine individual tolerance.

For autoimmune health, prioritizing whole food protein sources is generally best. Supplements can be a convenient and beneficial addition, especially for targeted gut healing (e.g., collagen) or to ensure adequate intake. However, a varied diet of wild-caught fish, grass-fed meats, and plant proteins should be the foundation.