Blueberry Protein Muffins
These blueberry protein muffins are moist, full of flavor and so easy to make. With protein from eggs, greek yogurt and protein powder, these are the perfect afternoon snack!

My banana protein muffins are still such a popular recipe, so I though it was about time to make a variation!
These blueberry protein muffins are moist, tender, gluten free and have 9 grams of protein per serving. They’re the perfect recipe to have on hand for quick snacks, whether after school, post-workout or when the late night chocolate cravings hit.
This recipe is oil free and made with simple, wholesome ingredients you probably already have on hand. If you love this recipe, try my protein waffles or gluten free protein bagel bites next!
Why you’ll love this recipe
- Easy to make
- 9 grams protein per serving
- Naturally gluten free
- Dairy free friendly

Key ingredients
EGGS. You need two whole eggs in this recipe which will help bind all ingredients together and ensure the muffins rise properly.
GREEK YOGURT. I love using greek yogurt in baking because it’s such an easy way to add both moisture and protein! To make these dairy free, I suggest the Kite Hill Greek Style yogurt.
APPLE SAUCE. Apple sauce will add moisture as well as some natural sweetness to these blueberry protein muffins.
SUGAR. I used white sugar to keep these a paler color, but you can use coconut sugar if you want them refined sugar free.
FLOUR. A mix of almond flour and oat flour will keep these gluten free! To make them nut free, just swap the oat flour with equal parts oat flour.
PROTEIN POWDER. I used a vanilla pea protein, which I recommend. I do not suggest chocolate or plain for the best flavor. Same with my banana bread protein cookies!

How to make blueberry protein muffins
Preheat the oven to 350 Fahrenheit and line a muffin tin with 10 liners and set aside. Note that this recipe just makes 10 muffins and not 12!
WANT TO SAVE THIS RECIPE?
In a mixing bowl, whisk together all wet ingredients until smooth.
Whisk in the dry ingredients, aside from the blueberries, until smooth and well combined. Fold in the blueberries.
Use a cookie scoop or spoon to scoop the batter into the muffin tin, filling each fairly close to the top. You should have 10 muffins.
Bake for 23-28 minutes or until a toothpick comes out clean. Let cool in the muffin tray for about 15 minutes, then transfer to a wire rack to finish cooling. Enjoy and try my mini protein cheesecakes next!

How to store and freeze
To store: Once prepared, these blueberry protein muffins will keep at room temperature for 3-5 days. I like to store them in a container or a ziplock bag to keep them moist.
To freeze: I have not tried freezing these muffins, but I do think that would work well! Be sure to let them cool completely, then transfer to a freezer safe bag and freeze for up to 1 month.
To reheat: If frozen, let the muffins defrost in the fridge, then reheat until warm through the center at 300. If they were simply in the fridge or at room temperature, just pop in the microwave for a few seconds to warm them up.

Tips for baking with protein powder
I love adding protein powder into pancakes, baked protein oats, muffins, protein donuts, cookies and even protein chocolate cake. I don’t recommend adding it into a traditional recipe, it’s important to follow a recipe that already calls for protein powder to ensure the texture holds up well.
Protein powder sort of acts like flour in baked goods, it will absorb excess moisture and add structure. When used in the right amount, it will keep the recipe nice and fluffy and flavorful.
Can I make them vegan?
Unfortunately, these blueberry protein muffins definitely need the eggs to hold together and rise properly. I do not recommend any egg swaps here since we need two eggs total, but you can instead try my vegan oatmeal muffins and swap 1/4 cup of the flour with protein powder.

More high protein recipes!
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Blueberry Protein Muffins
by: claire cary
Ingredients
Wet
- 6 tablespoons apple sauce
- ½ cup greek yogurt
- 2 eggs
- ¼ cup sugar
- 1 teaspoon vanilla extract
Dry
- ⅔ cup oat flour
- ½ cup almond flour
- ½ cup vanilla protein powder
- 2 teaspoons baking powder
- ¼ teaspoon salt
- ¾ cup fresh blueberries
Instructions
- Preheat the oven to 350 Fahrenheit.
- Line a muffin tin with 10 liners and set aside.
- In a mixing bowl, whisk together all wet ingredients until smooth.
- Whisk in the dry ingredients, aside from the blueberries, until smooth and well combined.
- Fold in the blueberries.
- Use a cookie scoop or spoon to scoop the batter into the muffin tin, filling each fairly close to the top. You should have 10 muffins.
- Bake for 23-28 minutes or until a toothpick comes out clean.
- Let cool in the muffin tray for about 15 minutes, then transfer to a wire rack to finish cooling. Enjoy!
Comments
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These are fire! I substituted the mashed banana for apple sauce because I didn’t have apple sauce, and that’s how I’ll make them going forward. Also, I subbed coconut sugar for granulated sugar, which isn’t much of a difference rather than the toll it takes on one’s blood sugar, and it’s great! Thank you for the best recipe. So far, my most favorite protein muffin recipe. <3
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Thank you, Katie! So glad you made them work for you.
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I just made this blueberry muffin recipe and it turned out great. I followed the recipe exactly besides substituting swerve for sugar. I have never used oat flour before and look forward to incorporating another recipes.
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Thank you, Lee!
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I make these with coconut flour instead of almond flour and noticed they’re kind of dry, would it be because of the flour or am I cooking too long
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You definitely cannot use coconut flour here! Almond flour and coconut flour behave very differently and will lead to dry muffins. Please follow the recipe as listed as I chose ingredients very carefully.
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Super moist and tasty. I added walnuts for extra protein!
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What can you replace applesauce with?
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You can use mashed banana instead!
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I’m so sorry; I recently asked about substituting gluten-free powder, but I realize the recipe is gluten-free. However, I meant to say substituting an all-purpose Gf flour for oat flour since I have an allergy. Or would you recommend using all almond flour? Thanks again!
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I’d probably use all almond flour!
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I used all almond flour because I didn’t have oat flour on hand, and they turned out mushy. Maybe the almond flour wasn’t absorbent enough. I’m going to follow the recipe with oat flour next time and see how they turn out.
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I’d recommend following the recipe as written for best results! Oat flour is usually more absorbent than almond.
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Hi there. Do I need to make any adjustments if I substitute Gluten-free flour? I am excited to try this recipe!
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I recommend sticking with the flour as listed!
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I did the muffins 10 times already, I love the recipe, they are super testy! And bless you for the metric button
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So glad you love them!
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Can I leave out the protein powder?
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I don’t recommend that – this recipe is designed to have the protein powder!
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I made your banana muffins and they were so good!! I quintupled the recipe! Now I want to try this, but is it possible to use frozen blueberries instead of fresh? It’s cheaper buying a huge bag of frozen blueberries than the fresh little bundles. Thanks!
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You can, but increase the bake time by a couple of minutes!
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Hi! What kind of protein powder did you use, whey or plant based? They work really differently in baked goods. Thanks!
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I usually use a vanilla pea protein!
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@eatwithclarity…these were so moist and delicious. My 15 yo is going to take them for school snacks. I used strawberry applesauce…so full of flavor! I used a blender to make my own oat flour.
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Love it! Thanks, Pama!
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These were delicious! I made a different recipe before this one and they were spongy with no flavor. This has flavor and is very moist and delicious
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Thank you, Rebecca!
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Hi Clare!
Can i use honey to replace the sugar?-
That should be fine!
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Hi! I plan on making these but I’m confused— you mention that it takes three eggs, but the recipe only lists two. Which is it?
Thanks!-
Two! Sorry, just updated that!
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