Healthy Blueberry Protein Muffins

Published by:
Liz Marino
| 05/27/2024 | Last Updated: 07/15/2025

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The Best Blueberry Protein Muffins Recipe! With 9g of protein per muffin – these protein muffins are easy to make and absolutely delicious!

A hand holding up a  blueberry protein muffin with a bite taken out of it.

If you’re trying to eat more protein, but still love sweets – you have to try these blueberry protein muffins! They’re a healthier, protein packed version of your favorite bakery treat with 9g of protein each!

Made with oat flour, Greek yogurt, whey protein powder and naturally sweetened with honey, these secretly healthy baked treats are the perfect packable snack or breakfast option for busy mornings.

These muffins are fluffy, full of flavor, easy to make in just 30 minutes and mixed up in one bowl for easy clean up! They are perfect for a quick breakfast or on-the-go snack.

For more blueberry breakfast options, try Blueberry Baked Oatmeal, Blueberry Banana Muffins, and Overnight Blueberry Oats.

liz’s tips on how to make blueberry muffins

  • When measuring the oat flour, be sure to use the “spoon and level” method to prevent overpacking. This is especially important when making homemade oat flour because it tends to compress a little while processing.
  • Adding the oat flour to the wet ingredients and mixing well allows the oat flour to absorb some of the moisture and get fully incorporated into the batter before the leavening agents are added (which prevents over activating the leavening). It also allows you to use one bowl for the entire recipe, which makes clean up so much easier.
  • Silicone muffin liners were tested and worked fine for this recipe. Because they are thicker and conduct heat a little less efficiently, silicone liners will take just a minute or two longer to bake. When using paper liners, be sure to allow the muffins to cool for at least 5-10 minutes before removing them from the liners so that they remove cleanly from the paper.
  • If your oven cooks unevenly, try rotating the muffin tin 180 degrees halfway through the cook time.

ingredients

Ingredients for Blueberry Protein Muffins in small bowls: greek yogurt, honey, eggs, avocado oil, oat flour, vanilla whey protein powder, baking powder, baking soda, salt, blueberries

It will also be helpful to have a nonstick muffin tin or silicone muffin liners

Substitutions

Greek Yogurt – I used non fat plain Greek yogurt, but I also tested whole milk Greek yogurt. Any fat percentage of plain Greek yogurt will work. I haven’t tried dairy free yogurt in this recipe so I don’t know how that would work.

Honey – Maple Syrup or even granulated sugar can be used instead of honey in this recipe. Granulated sugar seemed to brown a little faster and required a slightly shorter cooking time due to the change in moisture.

Eggs – I did not test any egg replacements in this recipe. If you try one, we would love to know how it worked in the comments below!

Avocado Oil – Any neutral flavored cooking oil can be used in this recipe, including light olive oil, or melted (and slightly cooled) coconut oil. If using coconut oil, allow eggs and Greek yogurt to come to room temperature before starting the recipe to prevent the coconut oil from solidifying.

Oat Flour– Store-bought oat flour or homemade oat flour can be used. I tested a variety of brands in this recipe, and all seemed to produce the same fluffy muffins. If using homemade oat flour, ensure the oats are processed into a very fine flour with no visible oats. Check out our post on how to make homemade oat flour for tips and tricks. If you need this recipe to be gluten-free, be sure to select gluten-free oat flour or gluten-free old-fashioned oats to make oat flour with.

Vanilla Whey Protein Powder – I tested two types of vanilla vegan protein powder in addition to vanilla whey protein and unflavored whey protein (with additional sweetener). While the vegan pea protein option functionally worked, I wouldn’t recommend using it because it tasted quite chalky, almost grassy, when paired with the oat flour. Review the notes on protein powder below to achieve the best for best results.

Baking Powder & Baking Soda – Both leavening agents are used in these protein muffins because Greek yogurt is acidic. With additional acid in the recipe, it requires an additional base to achieve a good rise.

Blueberries – I tested both fresh and frozen blueberries in this recipe. Both options worked great! If using frozen blueberries, do not thaw. Simply fold into the muffin batter and expect some slight color bleed.

Other Fruit – We also love these Strawberry Protein Muffins, Protein Banana Muffins, Apple Protein Muffins, and Pumpkin Protein Muffins.

How to Make Healthy Blueberry Protein Muffins

A clear bowl with muffin batter mixed together with blueberries on the side.
  1. In a bowl, combine the yogurt, honey, eggs, and oil. Whisk until smooth. Add in the oat flour and vanilla protein powder. Whisk in the baking soda, baking powder, and salt.
Blueberry Protein Muffin batter in a clear bowl with blueberries on the side.
  1. Use a rubber spatula to fold the blueberries into the batter.
Unbaked blueberry protein muffins in a muffin tin.
  1. Divide the batter into a lined muffin tin.
Baked blueberry protein muffins in a muffin tin.
  1. Bake at 350° for 16-20 minutes. Allow them to cool for about 10 minutes before enjoying.

Tips for selecting the best protein powder:

Whey Protein for baking:

I found that whey protein will generally work better for baking compared to vegan alternatives. Whey protein tends to have a simpler ingredient list and act more predictably when adding to a baking recipe. Vegan protein powders can be made from a variety of protein sources, so ingredients can vary quite a bit between brands.

When selecting a protein powder, I would recommend selecting one that contains whey protein, flavor, sweetener and maybe salt. Additional ingredients beyond that list will add additional variables to the recipe and you can expect slight variations in taste and texture. 

Vegan Protein for baking:

This vegan pea protein worked functionally in this recipe, meaning the muffins had a good rise and good texture, but I did not like the flavor it produced. When paired with the nutty flavors from the oat flour, it tasted grassy/earthy.

Chocho bean protein powder which worked really well when tested. I was a little nervous because, in smoothies, this type of protein is a little chalky and not very sweet, but it tasted great in this recipe. I have also heard rice protein powders are a good option to bake with but have not tried them. 

Unsweetened/unflavored protein powder can be used, but you will want to add additional sweetener and vanilla extract to the recipe. I tested using an additional 1/3 cup of honey plus 1 teaspoon of vanilla extract with unflavored whey and that worked, but because of the additional moisture this batch took longer to bake and were not as pretty but tasted good.

Brands that I have tested in this specific recipe: Iconic Protein Grass-Fed Whey in Vanilla Bean, Truvani Organic Vegan Protein Powder in Vanilla (would not recommend), Mikuna Chocho Protein Powder in Vanilla, Isopure Zero Carb Unflavored Whey Isolate

A pile of blueberry protein muffins with some in the background on a plate.

blueberry muffin recipe variations

  • protein packed mini blueberry muffins – Use a mini muffin tin and shorten the baking time.
  • muffins without protein powder – These Blueberry Banana Muffins are delicious and don’t contain protein powder!
  • using frozen blueberries – If using frozen blueberries, do not thaw. Simply fold into the muffin batter and expect some slight color bleed.
A blueberry protein muffin with a bite taken out of it on top of another muffin with more muffins in the background with blueberries on the side.

how to store muffins

Storing: These muffins can be stored in a gallon-size resealable zipper bag or container at room temperature. Allow muffins to cool fully before storing them in an airtight container to prevent condensation. Enjoy within 4 days for freshness.

Freezing: These blueberry protein muffins freeze really well. This is optional but I prefer to flash freeze them for about 20 minutes to prevent them from sticking together. You can do so by freezing the muffins inside the muffin tin after they have cooled at room temperature. Once partially frozen, place the muffins in a resealable freezer bag and store sealed for up to 1 month.

To Thaw: Simply pull the muffins from the freezer and thaw on the counter for about 24 hours, or pop one in the microwave directly from the freezer and microwave for about 30 seconds on high.

If you need more freezer friendly recipes check out our Fill Your Freezer Ebook.

Reheating: You can reheat these muffins in the microwave or toaster oven.

A blueberry protein muffin with a bite taken out of it with more muffins in the background.

Other high protein recipes:

If you want to eat more protein, get our free high protein meals guide. Here are some of our favorite high protein recipes:

A hand holding up a blueberry protein muffin with a bite taken out of it.

Blueberry Protein Muffins

Recipe by: Liz Marino
5 from 8 votes
The Best Blueberry Protein Muffins Recipe! With 9g of protein per muffin – these protein muffins are easy to make and absolutely delicious!
Prep Time : 10 minutes
Cook Time : 20 minutes
Total Time : 30 minutes
Serves : 12 muffins
(hover over # to adjust)

Ingredients

  • ¾ cup fat-free plain Greek yogurt 180 g
  • 2/3 cup honey 220 g
  • 2 large eggs
  • 1/3 cup avocado oil
  • 2 cups oat flour 220 g
  • ½ cup vanilla whey protein powder 30 g but will vary based on brand
  • 1 tsp baking powder
  • 1 tsp baking soda
  • ½ tsp salt
  • 1 cup blueberries 160 g

Instructions

  1. Preheat the oven to 350 F. Line a 12-count muffin tin with paper or silicone liners and set aside.
  2. In a large mixing bowl, combine the yogurt, honey, eggs, and oil. Whisk together until smooth.
  3. Add the oat flour and vanilla protein powder to the wet ingredients one at a time. Whisk together to full incorporate before adding the next ingredient.
  4. Sprinkle in the baking soda, baking powder, and salt. Whisk together to evenly distribute but avoid over-mixing.
  5. Use a rubber spatula to fold the blueberries into the batter.
  6. Using a 2-ounce scoop or large spoon, divide the batter between the muffin wells.
  7. Place the muffins in the oven and bake for 16-20 minutes (17 minutes was perfect for my oven).
  8. Remove the muffins from the oven and allow them to cool for about 10 minutes before enjoying.

Notes

Tips for this recipe:
  • You can make your own homemade oat flour by pulsing old fashioned oats in a blender until smooth
  • Whey protein powder works best in this recipe. Vegan protein powder can work but sometimes they taste chalky.
  • You can substitute honey with maple syrup.

Nutrition Facts

Serving: 1muffin | Calories: 235kcal | Carbohydrates: 31g | Protein: 9g | Fat: 9g | Saturated Fat: 1g | Polyunsaturated Fat: 2g | Monounsaturated Fat: 5g | Trans Fat: 0.003g | Cholesterol: 35mg | Sodium: 123mg | Potassium: 135mg | Fiber: 2g | Sugar: 18g | Vitamin A: 59IU | Vitamin C: 1mg | Calcium: 46mg | Iron: 1mg
Course: Breakfast
Cuisine: American
Tried this recipe?Share it! Make sure to tag @thecleaneatingcouple or use #thecleaneatingcouple!
5 from 8 votes

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Recipe Rating




14 Comments

  1. 5 stars
    We LOVE these muffins. Thank you for sharing.🫶🏻

  2. Linda Rothman says:

    Can I use almond flour for these muffins?

    1. No you can’t. Unfortunately oat flour can’t ever be substituted 1:1 with almond flour. It just won’t work! Almond flour has more fat than oats and interacts in baking totally differently.

  3. Annick Menard says:

    5 stars
    These were a great quick breakfast or snack

  4. 5 stars
    My favorite muffin recipe from y’all!! Thank you!

  5. These are so good. Great consistency too.

  6. Natalie Mills says:

    5 stars
    These muffins are delicious! Great idea for a quick breakfast or snack during the day. Kids loved them too!

  7. Lisa McConkey says:

    5 stars
    Excellent!! I have tried a few high protein muffins and this one has been the best! My goto recipe. Thank you!!

  8. 5 stars
    Just made these with a couple of substitutions to make them more WW friendly and they are awesome!
    I used sugar free maple syrup in place of the honey, and used equal parts of virgin olive oil and unsweetened apple sauce in place of the avocado oil.
    I will definitely hang on to this recipe.

  9. 5 stars
    I have been trying different recipes. This one is the best tasting and moist.

    Thank you so much for sharing!!

  10. 5 stars
    I haven’t made these yet, but I will and I will report back. The thing I most appreciate about Liz’s recipes is all the test testing that’s done before the recipe is posted. I have made many of Liz’s ( and Tyler’s) recipes and they are always delicious . If you read the entire recipe, they will tell you how other ingredients tested. There are no questions that you need to ask before making an item because it’s already there!! If they have not tried it, they will tell you. This takes a lot of time and patience and I am thankful for their hard work . When I read this recipe today I could not believe all the options that were listed. It makes it easy to pull up their recipes and start cooking . Thank you for having a great Instagram and website .