How to Find the Best Protein Powder for Autoimmune Disease

📌 Overview and Key Takeaways

This is a Dietitian’s guide on how to find the best protein powder for autoimmune disease.

Discover how to safely supplement your protein intake with autoimmune disease.

Last Updated
Jan 8, 2026

Author and Medical Reviewer

Written by Jack, Founder

Jack is the Founder of Drink Wholesome.

Medically reviewed by Brittany, MS, RD and Jenn, PA-C

Kayla is a Registered Dietitian with a MS in Nutrition.

Jennifer is a Physician Assistant with a BA in Nutritional Sciences.

Protein Powder for Autoimmune Disease

Is Protein Powder Good for Autoimmune Disease?

Autoimmune disease is a broad category of conditions where your immune system mistakenly attacks healthy cells and tissues.

Normally, your immune system’s primary function is to defend your body against pathogens.

In autoimmune diseases, however, it becomes confused and starts to identify your own cells and tissues as foreign threats.

Common examples of autoimmune disease include: rheumatoid arthritis, lupus, type 1 diabetes, multiple sclerosis (MS), hashimoto’s thyroiditis, celiac disease, psoriasis, and inflammatory bowel disease (IBD).

The Autoimmune Protocol (AIP) diet is a specialized diet designed to help individuals with autoimmune diseases manage their symptoms and potentially reduce inflammation in the body.

The primary goal is to eliminate foods that can trigger or exacerbate inflammation, immune responses, and gut-related problems, as these factors are often associated with autoimmune conditions.

It typically involves a strict elimination phase followed by a gradual reintroduction of foods to identify potential triggers.

Among the things it avoids are ultra-processed foods, refined sugars, oils, food additives, alcohol, caffeine, and certain medications.

During the elimination phase, many individuals also avoid foods such as grains, legumes, dairy, eggs, and nightshade vegetables.

Keep in mind that the AIP diet can be restrictive and challenging to follow, particularly during the elimination phase.

Ensuring a balanced intake of nutrients is also difficult and might require supplementation.

If you struggle to meet your protein needs, for example, protein powder can help you fill in gaps in your diet.

Finding an AIP-compliant protein powder is easier said than done, however.

What Is the Best Protein Powder for Autoimmune Disease?

If you are following the AIP diet, specifically the elimination phrase of the AIP diet, there are not many compliant protein powders.

Your only options are beef and collagen protein, which is made from the connective tissues of animals.

Once you complete the elimination phrase, your list of safe options grows to include most types of protein powder.

Not all of these protein powders are created equal, however.

In fact, most of them contain ultra-processed ingredients that could be problematic for individuals with autoimmune disease.

🚫 Avoid Food Additives

Regularly eating emulsifiers, thickeners, artificial sweeteners, and other ultra-processed additives can alter the composition and function of your gut microbiome (North Clin Istanb, 2019).

These shifts, known as gut dysbiosis, have been linked to the development of autoimmune diseases, including rheumatoid arthritis, multiple sclerosis, type 1 diabetes, systemic lupus erythematosus, and inflammatory bowel disease (Front Immunol, 2022).

Dysbiosis damages your gut barrier, changes what your gut microbes produce, and throws off immune function, all of which can contribute to autoimmune issues.

⚠️ Here is a list of the most common food additives in protein supplements:

• acacia fiber
• acacia gum
• acesulfame potassium
• artificial flavors
• ascorbic acid
• aspartame
• calcium carbonate
• carrageenan
• cellulose gum
• dextrin
• dicalcium phosphate
• dipotassium phosphate
• erythritol
• gellan gum
• guar gum
• gum arabic
• inulin
• locust bean gum
• maltitol
• maltodextrin
• mono- and diglycerides
• ‘natural’ flavors
• rice bran extract
• rice dextrin
• rice hulls
• rosemary extract
• silica
• silicon dioxide
• sodium alginate
• soluble corn fiber
• sorbitol
• soy lecithin
• sucralose
• sunflower lecithin
• tocopherols
• tricalcium phosphate
• xanthan gum
• xylitol
• zinc oxide

As a rule of thumb, if you cannot find it in nature or make it at home, it is probably a food additive.

🚫 Avoid Protein Concentrates and Isolates

If you have a sensitive stomach, you might also want to avoid ultra-processed protein concentrates and isolates.

Most protein supplements are made from one or both of these ultra-processed protein sources, which have been mechanically and/or chemically stripped of everything but the protein.

This includes the enzymes, fiber, and other natural digestive aids that help your gut break them down.

You therefore do not digest them in the same way that you do whole foods, which could affect your gut health.

Studies show that regularly eating protein concentrates and isolates might disrupt your gut microbiome (Nutrients, 2018) and cause the formation of toxic byproducts in your gut (Mol Nutr Food Res, 2024).

Individuals with pre-existing digestive issues should thus look for protein supplements made from whole food protein sources like egg whites and almonds, which are easier to digest and absorb.

Order Samples to see for yourself.

Sources

1. Northern Clinics of Istanbul (North Clin Istanb). Food additives and microbiota. 2019.
2. Frontiers in immunology (Front Immunol). Microbial dysbiosis in the gut drives systemic autoimmune diseases. 2022.
3. Nutrients (Nutrients). Effect of a Protein Supplement on the Gut Microbiota of Endurance Athletes: A Randomized, Controlled, Double-Blind Pilot Study. 2018.
4. Molecular nutrition & food research (Mol Nutr Food Res). In Vitro Fermentation of Animal and Plant Protein Isolates by the Human Gut Microbiota Under High and Low Carbohydrate Conditions. 2024.

Editorial Guidelines

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This article was written by a Registered Dietitian and reviewed by a Physician Assistant. We rely on peer-reviewed research and trusted medical sources, and regularly update our content to ensure accuracy and clarity.