These Cottage Cheese Blueberry Muffins are about to be your new favorite! They’re soft, packed with juicy blueberries, and have a sneaky boost of protein thanks to the cottage cheese. Plus, they are ready in just 30 min and stay soft for days. You can bake a batch and enjoy them all week. Trust me, once you try these, you won’t go back to traditional blueberry muffins!

I’ve been sneaking cottage cheese into everything lately, and these Blueberry Cottage Cheese Muffins might be my favorite yet! They’re super easy to make, and the cottage cheese keeps them soft and fluffy without making them taste like cottage cheese at all—I promise!
They’ve also got a nice boost of protein, so they keep you full instead of just giving you a sugar crash. I love that they come together fast with simple ingredients, and they’re perfect for breakfast, snacks, or, let’s be real, eating straight from the pan while they’re still warm.
If you are looking for more wholesome dessert recipes, check out my Cottage Cheese Banana Bread, Chocolate Chunk Banana Bread, or Sourdough Apple Muffins. You may also enjoy my easy cottage cheese recipes, like Cottage Cheese Mac And Cheese, or Mashed Potatoes With Cottage Cheese.
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Why You'll Love This Recipe
- Real, Wholesome Ingredients: These delicious muffins are made with simple, high-quality ingredients you can feel good about. Using real, whole foods not only makes them more nutritious but also enhances their flavor, giving you a muffin that tastes as good as it is good for you!
- Easy To Make: All you have to do is mix, bake and enjoy!
- Perfect For Meal Prep: Make a batch over the weekend and have a quick grab and go snack ready all week long.
Ingredients
- Gluten-Free Flour & Almond Flour: To keep these muffins gluten-free, I use a 1:1 gluten-free flour like Bob's Red Mill. I also like to use a little bit of almond flour as it helps make the muffins nice and chewy. If you don't want to make them gluten-free you can use all purpose flour instead.
- Sea Salt: Just a pinch of salt helps enhance all of the flavors and balance out the sweetness.
- Baking Soda: You'll need baking soda for these muffins, not to be confused with baking powder!
- Cinnamon: I love cinnamon in baked goods! It adds a touch of warmth and pairs beautifully with the blueberries.
- Unsalted Butter: I recommend using a grass-fed butter, like Kerrygold. The butter adds richness and moisture to the muffins while giving them a soft, fluffy texture. Using unsalted butter lets you control the salt level in the recipe.
- Coconut Sugar: Coconut sugar gives these classic muffins a gentle sweetness without refined sugar.
- Eggs: Use pasture raised organic eggs for best results. You will want to make sure the eggs come up to room temperature.
- Vanilla Bean Paste: I like using vanilla bean paste, but vanilla extract will work just fine.
- Cottage Cheese: The secret ingredient! Cottage cheese is a great way to add protein and it helps create a moist muffin. You won’t even know it’s there! You can use full-fat or low-fat cottage cheese, but make sure you use a good quality brand, like Good Culture.
- Blueberries: This recipe is best when fresh blueberries are in season. Do your best to buy organic if you can.
- Lemon Zest: A little bit of lemon zest brightens up the muffins, the combination of blueberries and lemon zest is fantastic! If you don't have a lemon on hand to zest, it's not a deal breaker.
See the recipe card for full information on ingredients and quantities.
Substitutions And Variations
- Cottage Cheese: If you're not a fan of cottage cheese, you can swap it out for Greek yogurt or coconut yogurt. It will still provide the additional moisture that you'd get from creamy cottage cheese.
- Butter: You can swap the butter for ghee, or coconut oil.
- Coconut Sugar: Feel free to replace the coconut sugar with maple syrup, date sugar or brown sugar.
- Berries And Nuts: If you are not a fan of blueberries, you can use fresh raspberries or fresh strawberries. You could also mix in your favorite nuts.
How To Make Blueberry Cottage Cheese Muffins
This is an overview with step-by-step photos. Full ingredients & instructions are in the recipe card below.
Step 1. Preheat your oven to 350 degrees f. Line your muffin pan with individual parchment paper liners.
Step 2. Add the gluten-free flour, almond flour, sea salt, baking soda, and cinnamon to a medium bowl and whisk to combine.
Step 3. Next add the cooled melted butter, sugar, eggs, vanilla, and cottage cheese to a large bowl and whisk to combine.
Step 4. Gradually add the dry ingredients to the wet ingredients and mix until almost combined.
Step 5. Use a spatula or wooden spoon to gently fold in the blueberries and lemon zest. Reserve a few blueberries for topping the muffins.
Step 6. Use a cookie scoop to scoop the muffin batter into the muffin cups. You will want to fill them about ¾ of the way full. Add a few extra blueberries and a pinch of coconut sugar or turbinado sugar to the top of the muffins for a little crunch. Place the muffin tin in the preheated oven and bake for 15-20 minutes, or until cooked through and golden brown.
Expert Tips And Notes
- Zesting The Lemon: For the best flavor, zest only the bright yellow outer layer of the lemon—avoiding the bitter white part underneath. A microplane works best for getting fine, zest without any bitterness.
- Don't Overmix The Batter: Mix the wet and dry ingredients until just combined—it's okay if you still see a few streaks of flour. Once you fold in the blueberries, everything will come together. Overmixing can lead to dense muffins, so keep it light and gentle!
- Toss The Blueberries In Flour: To help prevent the blueberries from sinking to the bottom of the muffins, gently toss them with 1 teaspoon of gluten-free flour before adding them to the batter.
- Use Muffin Liners: I highly recommend using parchment paper muffin liners. It makes for easy clean-up and a chic presentation.
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Serving Suggestions For Cottage Cheese Blueberry Muffins
- Toppings: Spread with a little smoked butter or homemade almond butter for a creamy touch, or drizzle with honey for added sweetness.
- Breakfast Pairings: Enjoy with a high-protein egg bake, or serve alongside a cottage cheese and fruit breakfast bowl for a well-rounded breakfast.
- Snacks: Pair with a handful of nuts for a satisfying midday snack, or enjoy with a protein smoothie for a post-workout boost.
- Beverages: These muffins go perfectly with an Iced Maple Latte, a warm Chai Tea, or a classic cappuccino. For a refreshing option, pair with an iced matcha or berry smoothie.
Storage And Reheating
- Storage: Store leftovers in an airtight container in the fridge for up to 5 days.
- Freezing: These muffins are great for freezing. Store them in a freezer bag and freeze for up to 3 months. To thaw, place them in the fridge overnight.
- Reheating: To reheat, place in an oven-safe dish or on a baking sheet and heat for 5 minutes in a 250 degree oven.
Recipe FAQs
I would not recommend it. Frozen blueberries tend to carry a lot of moisture. Fresh, in-season blueberries are going to be your best option.
They have a natural sweetness from coconut sugar and blueberries, but they’re not overly sweet. If you prefer sweeter muffins, add an extra ¼ cup of coconut sugar.
Overmixing the batter can make the muffins dense. Be sure to stir gently until just combined.
Other Related Dessert Recipes
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Cottage Cheese Blueberry Muffins Recipe
Ingredients
- 1 cup Gluten-Free Flour + 1 teaspoon divided
- ½ cup Almond Flour
- ½ teaspoon Sea Salt
- 1 teaspoon Baking Soda
- 1 teaspoon Cinnamon
- 6 tablespoons Butter unsalted melted
- ½ cup Coconut Sugar
- 2 Eggs room temperature
- 1 teaspoon Vanilla Bean Paste
- 1 cup Cottage Cheese
- 1 cup Blueberries
- 1 teaspoon Lemon Zest
Instructions
- Preheat your oven to 350 degrees. f Line your muffin pan with individual parchment paper liners.
- Add the gluten-free flour, almond flour, sea salt, baking soda, and cinnamon to a medium bowl and whisk to combine.1 cup Gluten-Free Flour + 1 teaspoon, ½ cup Almond Flour, ½ teaspoon Sea Salt, 1 teaspoon Baking Soda, 1 teaspoon Cinnamon
- Next add the cooled melted butter, sugar, eggs, vanilla, and cottage cheese to a large bowl and whisk to combine.6 tablespoons Butter unsalted, ½ cup Coconut Sugar, 2 Eggs, 1 teaspoon Vanilla Bean Paste, 1 cup Cottage Cheese
- Gradually add the dry ingredients to the wet ingredients and mix until almost combined.
- Use a spatula or wooden spoon to gently fold in the blueberries and lemon zest. Reserve a few blueberries for topping the muffins.1 cup Blueberries, 1 teaspoon Lemon Zest
- Use a cookie scoop to scoop the muffin batter into the muffin cups. You will want to fill them about ¾ of the way full. Add a few extra blueberries and a pinch of coconut sugar or turbinado sugar to the top of the muffins for a little crunch. Place the muffin tin in the preheated oven and bake for 15-20 minutes, or until cooked through and golden brown.
Notes
- Zesting The Lemon: For the best flavor, zest only the bright yellow outer layer of the lemon—avoiding the bitter white part underneath. A microplane works best for getting fine, zest without any bitterness.
- Don't Overmix The Batter: Mix the wet and dry ingredients until just combined—it's okay if you still see a few streaks of flour. Once you fold in the blueberries, everything will come together. Overmixing can lead to dense muffins, so keep it light and gentle!
- Toss The Blueberries In Flour: To help prevent the blueberries from sinking to the bottom of the muffins, gently toss them with 1 teaspoon of gluten-free flour before adding them to the batter.
- Use Muffin Liners: I highly recommend using parchment paper muffin liners. It makes for easy clean-up and a chic presentation.
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