How to Find the Best Protein Powder for Autoimmune Disease

📌 Overview and Key Takeaways

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

Discover how to safely meet your protein needs with autoimmune disease.

drink wholesome founder
Last Updated Jul 21, 2026
Author and Medical Reviewer

Jack, CNC

Jack is a National Academy of Sports Medicine Certified Nutrition Coach.

Jack’s Story | Jack on LinkedIn | Jack in Forbes 30 Under 30

Disclaimer: This communication is for general informational purposes only and is not a substitute for personalized medical advice.

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Protein Powder for Autoimmune Disease

Is Protein Powder Good for Autoimmune Disease?

Yes, protein powder can be beneficial for someone with autoimmune disease, as long as it is chosen carefully.

Autoimmune disease occurs when your immune system mistakenly attacks healthy cells and tissues.

Common examples include:

  • Rheumatoid arthritis
  • Lupus
  • Type 1 diabetes
  • Multiple sclerosis (MS)
  • Hashimoto’s thyroiditis
  • Celiac disease
  • Psoriasis
  • Inflammatory bowel disease (IBD)

Autoimmune disease can be managed by a combination of medical treatments and lifestyle strategies, including Autoimmune Protocol (AIP) diet.

In addition to helping manage symptoms, it might also help reduce inflammation, though evidence is limited (Inflamm Bowel Dis, 2017).

The primary goal of the AIP diet is to eliminate foods that can trigger immune responses.

It typically involves two phases:

  1. A strict elimination phase
  2. A gradual reintroduction of foods to identify potential triggers

During the elimination phase, most participants avoid ultra-processed foods, refined sugars, oils, food additives, alcohol, caffeine, and certain medications.

Some people also choose to avoid grains, legumes (beans and lentils), dairy products, eggs, and nightshade vegetables (tomatoes, peppers, eggplant, potatoes).

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

Getting a balanced intake of nutrients, it follows, might be difficult and require supplementation.

If you struggle to meet your protein needs in particular, protein powder can help you fill the gaps.

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

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What Is the Best Protein Powder for Autoimmune Disease?

If you are following the AIP diet, specifically the elimination phase of the AIP diet, you have limited protein powder options.

Your only options are beef protein powder and collagen protein powder, which are basically the same thing.

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

Not all protein powders are created equal, however.

In fact, most protein powders contain ultra-processed ingredients that could be problematic for people with autoimmune disease.

🚫 Avoid Food Additives

Regularly eating emulsifiers, thickeners, and other ultra-processed additives can alter the composition and function of your gut microbiome – the collection of bacteria and other microorganisms living in your digestive system (North Clin Istanb, 2020).

These shifts, known as gut dysbiosis, have been linked to the development of autoimmune diseases (Front Immunol, 2022).

Dysbiosis is so problematic because it can damage your intestinal barrier and disrupt your immune system function.

⚠️ Here is a list of the most common food additives in protein shakes and powders:

  • 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 protein concentrates and isolates.

Most protein shakes and powders 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 you break them down.

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

For example, one study shows that regularly consuming protein concentrates and isolates might disrupt your gut microbiome (Nutrients, 2018).

Another study shows that it could cause the formation of toxic byproducts in your gut (Mol Nutr Food Res, 2024).

Although further research is needed, individuals with sensitive stomachs can play it safe by choosing protein shakes and powders made from minimally-processed protein sources like egg whites and almonds.

They are more gut-friendly.

Order Samples to see for yourself.

Sources

  1. Inflammatory Bowel Diseases (Inflamm Bowel Dis). Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease. 2017.
  2. Northern Clinics of Istanbul (North Clin Istanb). Food additives and microbiota. 2020.
  3. Frontiers in Immunology (Front Immunol). Microbial dysbiosis in the gut drives systemic autoimmune diseases. 2022.
  4. Nutrients (Nutrients). Effect of a Protein Supplement on the Gut Microbiota of Endurance Athletes: A Randomized, Controlled, Double-Blind Pilot Study. 2018.
  5. 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


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

Frequently asked questions

Who Is Drink Wholesome for?

Drink Wholesome makes protein powder for sensitive stomachs, GERD, IBS, and other gut issues. It’s suitable for most food sensitivities, including lactose intolerance, and won’t cause side effects like bloating, constipation, and reflux.

Why Is Drink Wholesome Good for Sensitive Stomachs?

Drink Wholesome is the best protein powder for sensitive stomachs because it’s additive, dairy, and gluten-free. It’s also made from minimally-processed protein sources like egg whites and almonds. Other protein powders are made from ultra-processed protein concentrates and isolates, which look nothing like real food.

What’s the Difference Between Protein Powder and Meal Replacement Powder?

Drink Wholesome makes gut-friendly Protein Powders and Meal Replacement Powders. Protein powder is high in protein and low in everything else, whereas meal replacement powder contains fats, carbs, fiber, and protein because it’s intended to replace the nutritional value of a balanced meal.

What’s the Difference Between Almond, Collagen, and Egg White Protein?

We make three types of stomach-friendly Protein Powder: Collagen Protein Powder, Egg White Protein Powder, and Vegan Almond Protein Powder. As long as you get protein from a variety of sources, any type of protein can help you meet your total daily protein needs. In other words, for someone with a balanced diet, there is no advantage to consuming one type of protein over another. Order Samples to see which type you like the most.

Ask Nutrition Coach

If you’re wondering which Drink Wholesome product is best for you, ask our Certified Nutrition Coach. For personalized medical advice, consult your healthcare provider.

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High Protein Balls

PREP TIME

5 min

COOK TIME

5 min

SERVES

2

Ingredients
  • ⅓ cup Protein Powder
  • ½ cup nut butter
  • ¼ cup maple syrup
  • 1 tsp vanilla extract
  • ½ cup rolled oats
  • ¼ cup mini chocolate chips
  • ¼ cup shredded coconut
Instructions

Combine the Protein Powder, nut butter, syrup, extract, and oats in a food processor or blender. Pulse until well combined. Add the chocolate and coconut, and pulse a few more times. Roll the dough into 10 balls. Enjoy!