Blueberry Protein Muffins Recipe
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You’ll love these higher protein muffins these Protein Blueberry Muffins are a delicious, healthy breakfast bursting with blueberry flavor. Plus, they are quick and easy to make! Try baking a batch this weekend and serving them for breakfast throughout the week.

Cottage cheese is having a moment. My kids have always loved cottage cheese but to be honest, it’s not usually my favorite. However… the idea of adding it to muffins and boosting it with some added protein, I’m here for it!
Blueberry Protein Muffin Recipe
On our sister site, Joyfully Mad, we have tons of muffin recipes, but when I thought about creating something for this site, I wanted to make sure it had more oomph to it than a classic muffin recipe.
It turns out when you add cottage cheese into the base of a muffin recipe, you get a boost of flavor, moisture, AND protein without even tasting the cottage cheese at all 😉
Why You’ll Love These Muffins
- The cottage cheese and eggs make these muffins more protein-rich compared to standard muffins. All purpose flour adds to the protein content too!
- They’re a great way to plan ahead for your week! Make a batch to meal prep for breakfast or snacks.
- No protein powder required! So many protein muffins require protein powder but that can drastically change the texture. Ours just uses natural ingredients to boost the protein content! You can add protein powder to these if you’d like, though, and we’ll teach you how below.
Ingredients
The ingredients for these muffins are so simply, with the exception of cottage cheese you might even have it all right at home! Here’s what you’ll need to make these.

- Eggs
- Coconut oil: Using coconut oil in the recipe adds moisture and a hint of coconut flavor to the batter. Make sure the coconut oil is fully melted before adding it to the batter for even mixing. Substitute another neutral oil like avocado oil if you need to!
- Milk: Feel free to use whatever milk you have on hand. Full-fat milk will create a richer, creamier result. 2% will create a lighter muffin. I don’t recommend using fat-free milk, as the recipe can turn out dry.
- Brown sugar or coconut sugar: Rather than using white sugar, I use brown sugar in this recipe for its rich, deep flavor. Coconut sugar is another fantastic choice.
- Vanilla extract: This adds a lovely flavor and a comforting, warm scent to the muffins!
- Cottage cheese: To make this recipe dairy free, you can use a vegan cottage cheese. It will bake similarly to regular cottage cheese.
- All-purpose flour: These muffins are not gluten free as written. Make sure to check out the Substitions and Variations section below for tips on how to adapt this recipe!
- Baking powder: This helps the muffins to rise. I wouldn’t substitute this ingredient.
- Cinnamon: This adds sweet, warm flavor to the recipe. If you aren’t a fan of cinnamon, try using another warm spice like nutmeg or cardamom. Use 1/4 teaspoon if you’re substituting, as these spices have a stronger flavor.
- Salt: Regular table salt works perfectly in this recipe. No need to buy anything special!
- Blueberries: You can use fresh blueberries or frozen blueberries for this recipe. No need to defrost first, you can use them frozen.
When baking, using room temperature ingredients can help your batter mix well. Before you begin measuring everything out, take your eggs and cottage cheese out and let them come to room temperature while you prepare the rest.
Substitutions and Variations
Gluten free muffins: If you would like to make this recipe gluten free, I recommend using a 1:1 gluten free flour blend.
Protein powder: You can substitute some of the flour with vanilla protein powder or pea protein. Replace 1/4 to 1/3 cup of the flour with protein powder. Depending on the type of protein powder you use, you may need to adjust the liquid content slightly. If the batter seems too thick, add a tablespoon or more of extra milk to reach the desired consistency.
Collagen: Add a scoop of your favorite unflavored collagen powder for an extra 10 grams of protein (on average). We love the one from Thrive Market!
Get 30% off your first order plus a free gift when you sign up for Thrive Market!
Different fruit: You can try other fruit in this recipe, like raspberries or blackberries. Strawberries would work too but tend to not have the same sweetness when baked as other fruit.
How to Make Blueberry Protein Muffins
- Preheat oven to 375º and line a muffin tin with liners or spray. In a medium bowl, whisk together brown sugar, coconut oil, milk and vanilla until combined.
- Add in eggs and cottage cheese and whisk again until combined.
Note: If you want to make the cottage cheese less clumpy in your batter, blend it real quick before adding it to the rest of the ingredients for a more yogurt-like consistency.
- In a separate, larger bowl whisk together dry ingredients (reserving 1 teaspoon of flour).
- Combine the wet and dry ingredients and mix until just combined (be sure not to overmix or you will end up with dense muffins!)
- Toss blueberries in remaining tablespoon of flour, then fold in blueberries to muffin batter. The batter will be thick!
- Scoop about ¼ cup of batter into each muffin tin and bake for 22-24 minutes, until the tops are golden brown and bounce back when gently pressed.
Allow to cool in muffin tin for 3-4 minutes before removing from muffin tin and cooling completely on cooling rack.

What to Serve with Blueberry Protein Muffins
While these muffins can be a great full meal on their own, they're great paired with the following suggestions:
I love serving Greek yogurt alongside the muffins for extra protein! For an added touch, try topping the yogurt with homemade maple pecan granola.
Serve them with your favorite morning smoothie, like this strawberry pineapple smoothie or this mango banana smoothie.
You can also pair your muffins with some crisp air fryer bacon!

Tips for Success
Do the toothpick test. When the muffins are done, a toothpick inserted into the center of the muffins will come out mostly clean. This means the muffins are fully baked and ready to remove from the oven. You don't want the toothpick to be DRY though or your muffins will be, too.
Line your muffin tins. To reduce cleanup time, line your muffin tin with silicone muffin liners or paper muffin liners. If you aren’t lining, make sure to grease your muffin pan well!
Check for color. The tops of the muffins should be golden brown when they’re done baking, giving them a lightly crisp texture while keeping the interior moist and fluffy.

FAQ
Allow the muffins to cool completely. Then, place the blueberry muffins in an airtight container and store them at room temperature for 2-3 days or in the fridge for up to 5 days.
Absolutely! You can make the muffins ahead of time and store them in an airtight container. For longer storage, freeze the muffins and thaw them as needed for a quick breakfast or snack.
Muffins freeze beautifully. To freeze, allow them to cool completely, then wrap them individually in plastic wrap or place them in a freezer bag, removing as much air as possible. They can be stored in the freezer for up to 3 months. To thaw, pop them in the microwave for 20-30 seconds or until fully defrosted.
More Breakfast Recipes
- Almond Flour Banana Muffins
- Hashbrowns in Air Fryer
- Air Fryer Hard Boiled Eggs
- Turkey Bacon in Air Fryer
I'd love to hear about your experience making this recipe! Please leave a comment and rating below!

Blueberry Protein Muffins Recipe
Equipment
Ingredients
- ½ cup brown sugar or coconut sugar
- ¼ cup coconut oil
- ¼ cup milk
- 1 teaspoon vanilla
- 2 eggs
- 1 cup cottage cheese
- 1 ½ cup all purpose flour + 1 teaspoon reserved
- 1 tablespoon baking powder
- ½ teaspoon cinnamon
- ¼ teaspoon salt
- 1 cup blueberries
Instructions
- Preheat oven to 375º and line a muffin tin with liners or spray.
- In a medium bowl, whisk together brown sugar, coconut oil, milk and vanilla until combined. Add in eggs and cottage cheese and whisk again until combined.
- In a separate, larger bowl whisk together dry ingredients (reserving 1 tablespoon of flour).
- Combine the wet and dry ingredients and mix until just combined (be sure not to overmix or you will end up with dense muffins!)
- Toss blueberries in remaining tablespoon of flour, then fold in blueberries to muffin batter. The batter will be thick!
- Scoop about ¼ cup of batter into each muffin tin and bake for 22-24 minutes, until the tops are golden brown and bounce back when gently pressed.
- Allow to cool in muffin tin for 3-4 minutes before removing from muffin tin and cooling completely on cooling rack.