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What Protein Powder is Best for a Healthy Gut?

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Although some forms of protein powder can be hard on the digestive system, there are healthy protein powder options that actually promote digestion and provide other health benefits.  So what protein powder is best for a healthy gut? Keep reading to find out.

Healthy protein powders flavored chocolate and vanilla

Reading Time: 6 minutes

What protein powder is best for a healthy gut? Keep reading to find out…

Over the past several years, protein powders have seemed to gain a poor reputation. Although some forms of protein powder can be hard on the digestive system, there are various healthy protein powder options that actually promote digestion and provide other health benefits. 

In my work with autoimmunity and gut health, I’m frequently asked about the benefits (and consequences) of protein powder:

“Is protein powder healthy?”

“What protein powder is best?”

“Is protein powder safe for me?”

As with almost everything else, quality is key. Certain protein powders (as discussed below) are better for your body than others, especially when poor gut function or autoimmunity is at play. 


In my professional opinion, protein powder can play an important role in most healthy, balanced diets- even when extenuating health circumstances are present. Protein plays an essential role in the body, as it’s responsible for building and maintaining muscle mass, providing energy, healing infections, and much more. 

The benefits of healthy protein such as healing the gut lining

Despite its impressive workload, adequate protein is lacking in the average American diet. Enter: protein powder. High quality protein powder is an effective and delicious way to consume more protein on a daily basis. When it comes to the gut health and autoimmunity, protein powder can help:

  • Heal the gut lining
  • Provide essential vitamins and minerals 
  • Reduce inflammation
  • Boost the immune system

That being said, choosing the right protein powder is often easier said than done. 

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When you walk into any grocery store or supplement shop, you’ll probably see protein powder galore. The options seem endless! However, finding the right option isn’t always such an easy task.

Choosing the right protein powder is key if you struggle with GI distress (bloating, gas, indigestion), are in the process of healing your gut, or have an autoimmune condition. I encourage you to stick to these tips when shopping for protein powder:

Things to look for when choosing healthy protein
Skip the Whey

Not to state the obvious, but whey protein powder is made from dairy. If you’ve struggled with gut issues or autoimmunity for awhile, you’re probably familiar with the distress dairy can cause in your tummy. But, that’s not all. When the gut and immune systems aren’t up to par, dairy can cause overall inflammation in the body. 

Quality Over Quantity

Don’t let labels that state “natural” or “organic” fool you. Most of the time, these marketing tactics aren’t anything more than false advertising. Instead, here’s what you should look for:

  • Purity- Protein powders are NOT all created equally. Most plant based protein powders contain a high amount of heavy metals and contaminants. These products are usually the protein powders you can find in grocery stores and health food shops. 
  • Quality- Look for brands that willingly share their reports with full transparency. Your protein powder should be tested specifically for heavy metals and contain only non-GMO, organic ingredients. Actually, The Clean Label Project completed a study that revealed 130 types of toxins in over 134 different protein powders. This is something to especially be aware of in plant-based powders. Note: if you suffer from autoimmunity, it’s essential to avoid food sources of heavy metals. 
Minimal Ingredients

Protein powders often have way too many ingredients, which isn’t ideal for those with leaky gut and autoimmune conditions. Most of these ingredients include binders, fillers, gums, prebiotics, and sweeteners. While these ingredients aren’t inherently bad, they frequently cause GI distress, like bloating and gas.


Following my checklist above, I’ve selected the healthiest protein powders that are approved for those with gut issues and autoimmune disease:

Best protein powders for gut health, best brands of protein powder, top 6 protein powders
1. Equip Protein

This is my number one overall suggestion for gut health and to support autoimmune conditions. I also think it is the best tasting quality protein powder I’ve found! Prime Protein from Equip contains 21g of bioavailable protein from grass fed beef. The amino acid profile in hydrolyzed beef protein can’t be compared to any other protein source and is why I choose it to support healing. It has such simple ingredients with no added chemicals, fillers, binding agents or artificial coloring or sweeteners. I suggest going with the chocolate or vanilla flavor, as the ingredients are very basic. If you are currently experiencing gut distress or in an autoimmune flare, the unflavored variety would be best. I highly recommend this one for your morning smoothies and recipes! 

2. PurePaleo by Designs for Health

PurePaleo was made with autoimmunity in mind. It’s made with hydrolyzed beef bovine protein, which is easy to digest and high in protein. It also contains all essential amino acids which support gut health. I always recommend going with the plain unflavored version of this one since it only has one ingredient. The plain flavor is a great option when you add some natural sweeteners such as raw honey or maple syrup and add to smoothies, oatmeal, or baked goods! 

3. Perfect Protein

Perfect Protein is an excellent, newer option that I typically suggest for those specifically with Small Intestinal Bacterial Overgrowth (SIBO) since it is low fodmap. I ove that it is highly regulated and lab tested for purity and heavy metals, which is a key factor when choosing the right protein powder and important when healing the gut. The ingredients are plant based and vegan, including protein rich sources like, pumpkin seed, hemp seed, and sacha inchi. Bonus: you won’t find any binders or fillers! Since it is naturally unflavored, you might find adding some raw honey or maple syrup enhances the taste.

4. Nuzest Clean Lean Protein

Nuzest Clean Lean Protein would be my recommended option for those who need an alternative to a hydrolyzed beef protein. It is made from European golden peas and is easy to digest, resulting in improved bloating and discomfort. This protein is plant based and vegan, allergen free for sensitive individuals, and it is clean enough to help gut dysfunction and autoimmunity. The ingredients are minimal using no chemicals, additives, or preservatives. On top of this, batches of Clean Lean Protein are regularly tested for safe microbial activity, allergenic substances, and heavy metals. Everything is certified gluten-free and GMO-free. While Nuzest is still one of my favorites, they recently reformulated, resulting in a slightly different taste. 

5. GI Replenish

GI Replenish is a great option for those with active, more severe IBD/IBS symptoms. It contains the essential amino acids, along with L-Glutamine which acts as a primary fuel source for the enterocytes (the cells lining the intestines), promoting their health and encouraging the regeneration of the gut lining. This is crucial for individuals with leaky gut syndrome, where the integrity of the intestinal barrier is compromised. Clinical studies have shown that supplementation with L-Glutamine can help in strengthening the gut barrier function and reducing inflammation, thereby reducing the permeability of the intestines and the exposure to antigens that could potentially trigger or exacerbate autoimmune conditions. Many of my clients describe this protein as drinking a milkshake because it tastes thick and creamy!  


While there are many protein powder options available, it’s worth figuring out the right option for your body, needs, and goals. At the end of the day, you want to support your body, not harm it. Once you’ve chosen the right protein powder for you, grab my Ultimate Smoothie Recipe Booklet so you can start to incorporate your protein powder for breakfast, lunch, dinner, and/or snacks! 

If you need more help figuring out what protein powder is best for you, I encourage you to work with a functional practitioner who can make this important decision with you! I would love to hear what protein powder you decide to go with to support your gut health. Leave a comment below and let’s start a conversation!

  1. Ann says:

    Hi Nikki,

    I just found your site after having a Dietary Consult. I have not been tested for Fructose Intolerance but my Dietician recommended a protein powder with too many ingredients including fake sugar I am sensitive too. I struggle with CIC (Chronic Idiopathic Constipation) and attend PFT (pelvic floor therapy). I will go for 3 days without a bm. Which of the protein powders would be good to start? I didn’t know if I should avoid pea protein or try it. Thank you for the advice!


    • Nikki Yelton says:

      Hi Ann! Thanks for reaching out. I am really glad you are working with someone who can help you along, it sounds like you are making your health a priority which is awesome! I would start with something very minimal and basic. With all the options I listed above, the Pure Paleo or the Nuzest Clean Lean Protein (which is European pea) might be best to start with. It would also help to make sure your smoothie is nice and balanced with the right ratios of protein, fats, carbs, and fiber to help constipation as well. The recipe above can give you an idea of what that might look like. Let us know how you do!

  2. Lindsay says:

    Hi maybe you can recommended one for me. I have hashimotos. I’ve gone gluten free, dairy free, etc. I was doing just a bone broth protein powder but I’m now questioning if I have a histamine intolerance. Any recommendations?

    • Nikki Yelton says:

      Hi Lindsey!

      Thanks for reaching out. I am glad you stumbled upon this article! So I can’t give personalized recommendations unless you are a client and I know more about your unique chemistry through testing but I will tell you it is very common to have SIBO with Hashimotos. This can cause higher histamine until the gut is healed the right way and this could be why you would experience bloating and some discomfort with the bone broth protein even though this is the golden recommendation for those with autoimmunity. This is where it is always great to personalize based on your unique body! With that being said, I find most women do very well on the plain Perfect protein linked in the article above OR the Nuzest Clean Lean Protein also mentioned above. I would suggest experimenting and see what works best for you body. Another thing that can really help is to cycle your protein. This might look like the bone broth protein 2-3 days a week and maybe the Nuzest on the other days.

      I hope all this helps, let us know how you do!! 🙂

  3. Susan says:

    Which protein powder do you suggest for someone with SIBO, who is also looking to gain weight?

    • Nikki Yelton says:

      So I actually mention the Perfect protein in this article and that is usually my go to for anyone with SIBO. When it comes to gaining weight, making sure you have your protein with a balanced smoothie can really support healthy weight gain or loss (whichever way you need to go). I would suggest searching “smoothie” in the blog homepage search bar for an article I wrote that teaches you how to balance your smoothies the right way to ensure you are getting the amounts you need. I hope that helps, let me know how you do!

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