High Protein Blueberry Cottage Cheese Muffins
- Autumn Bates, CCN, MS, BS, CPT
- Jul 2
- 7 min read
This post may contain affiliate links. Please read our disclosure policy.
These soft and fluffy blueberry cottage cheese muffins are about to be your new go-to. They're naturally gluten-free, low carb and come packed with 10 grams of protein per muffin, making it the perfect addition to your breakfast or lunch.

I have been eating cottage cheese every single day for about three years. Usually it's in the form of a cottage cheese bowl (like my viral blueberry cottage cheese bowl recipe), but today I wanted to switch it up and whip up some muffins instead.
There are a lot of recipes using cottage cheese in baked goods, but many of them fall short, nutritionally speaking. Those recipes often use regular wheat flour and a significant amount of sugar in addition to cottage cheese, making it not much healthier than a regular ol' muffin.
I set out to make a muffin recipe that actually contained a significant amount of protein while also being free from processed wheat flour.
My blueberry cottage cheese muffins have very little added sugar and come packed with 10 grams of protein per serving. With only 15 net carbs from whole food sources, these muffins are more in line with wellness and fat loss goals.
Even with all of those benefits, it's still shockingly light, fluffy and bursting with flavor.
Whether you're on a wellness journey or not, this is one cottage cheese recipe you're going to want to test out (and probably make every week).

What's In This Post
Recipe Highlights
Rich in protein and low carb. Each muffin contains 10 grams of protein with only 15 net carbs.
Naturally gluten-free. None of the ingredients naturally contain gluten. But if you're celiac or very sensitive to trace amounts of gluten then make sure to opt for certified gluten-free ingredients (such as oats).
Minimal added sugar. By using mashed bananas and vanilla protein powder, we're able to keep the added sugar extremely low.

Key Ingredients
Cottage Cheese
Cottage cheese ramps up the protein while also adding in nutrients like vitamin K2 and calcium for bone, dental and heart health. Make sure to opt for a full-fat (whole milk) cottage cheese. Studies have found that those who eat full-fat dairy products are less likely to be obese. Plus, the vast majority of vitamin K2 is only found in the fat.
To maximize for health, taste and weight loss perks, go for full-fat, not low-fat.
Oat Flour
Instead of processed wheat flour, we're using oat flour. Oat flour has a low glycemic load which means it's more blood sugar stabilizing and less likely to cause cravings later in the day. I like to take whole oats and grind them in an herb or coffee grinder until a fine powder forms.
Autumn's Vanilla Protein Powder
Our zero added sugar vanilla protein powder adds the perfect touch of sweetness to these muffins while also significantly boosting the protein content. The light vanilla flavor enhances the blueberry goodness without overpowering it. By adding in our protein powder, we're able to keep the sugar and carbs low while still getting a punch of protein to help promote a fat loss goal.
You can find our delicious Vanilla Protein Powder to use in this recipe HERE.
Greek Yogurt
The amount is small, but don't skip it! Greek yogurt helps to prevent drying that can occasionally happen when cottage cheese is used in baked goods. Just like with cottage cheese, make sure to use full-fat (whole milk) greek yogurt.
Equipment Needed
Handheld immersion blender: This is to blend the cottage cheese into a smooth consistency. I've found a handheld immersion blender to be best at this, but you can try using a food processor or blender as well. These will be much more messy to clean up and might not provide as smooth of a consistency as the handheld immersion blender. The one I have is very old, but you can find a similar handheld immersion blender here.
How To Make These Muffins
Although these muffins aren't difficult to make, there are a few steps to ensure the fluffiest, most delicious end result.
Step 1: Blend the cottage cheese.
Blending the cottage cheese until smooth helps prevent clumps in your muffins. It also makes the batter smooth and the final muffin much more fluffy. I used a handheld immersion blender which only took about 5 seconds of blend time.

Step 2: Mix the dry ingredients.
Combine all of the dry ingredients in one bowl and whisk. This allows for an even distribution of the ingredients..

Step 3: Mix the wet ingredients.
In a separate bowl, mix all of the wet ingredients. Just like with the dry ingredients, this ensures the wet ingredients are evenly mixed in so you don't get a clump of vanilla extract or egg in a bite of muffin.

Step 3: Combine the wet and dry ingredients.
I used a rubber spatula to fold the two mixtures together. You don't need (or want) to over mix it, so just mix the batter until you no longer see clumps of flour.

Step 4: Fold in the blueberries.
Using the same rubber spatula, fold in the blueberries. I like to save a few blueberries to top at the end when I fill the muffin tins.

Step 5: Fill your muffin tins and bake!
Make sure to only fill each muffin tin about 3/4 of the way. This prevents the muffins from spilling over as it rises in the oven. Bake for 22-25 minutes or until a toothpick comes out clean. They should be lightly golden on top when done.

Ingredient Swaps
Eggs: If making this egg-free, you can swap out the eggs for flax or chia eggs. Just mix one tablespoon of ground flax or chia seed with three tablespoons of warm water per egg used. Let this sit for a few minutes before adding it into the mixture. Keep in mind, swapping out the eggs will reduce the overall protein content.
Oat flour: I prefer using oat flour to keep the glycemic load lower. However, if swapping in other flours, you can usually use a 1:1 ratio.
Blueberries: If you don't have blueberries on hand, you can use raspberries, strawberries or blackberries. Just make sure to chop up the fruit you're using to roughly match the size of blueberries.
Protein powder: You can sub out the protein powder for the same amount of oat flour. However, keep in mind this will significantly lower the protein content and likely reduce the sweetness of the muffins.

Storing and Reheating
You can store these muffins in a glass container in the fridge for up to 5 days. I personally like eating them cold, but you can also reheat them in the microwave for 20-30 seconds.
FAQ's
When is the best time to eat these muffins?
If you're working toward a fat loss goal, I don't recommend eating these muffins as a snack. Instead, eat them with a meal. For example, you could pair two muffins with two hard boiled eggs for a complete meal. Or you could have one muffin with a high protein smoothie.
Can I add cottage cheese to blueberry muffins?
Absolutely! But I recommend blending the cottage cheese until smooth first to prevent clumpy muffins.
Is it better to use fresh or frozen blueberries?
Either can be used, but I prefer frozen. These are less expensive, available year round and tend to be picked at peak ripeness, ensuring the best flavor.
Other Breakfast Recipes You May Love
Love this recipe? Let me know in the comments below!

Blueberry Cottage Cheese Muffins
Makes 12 muffins, 1 muffin per serving
Ingredients:
1 cup oat flour
1/2 cup Autumn's Vanilla Protein Powder
1/4 cup almond flour
1 teaspoon baking powder
1/2 teaspoon baking soda
1/2 teaspoon ground cinnamon
1/4 teaspoon salt
3/4 cup cottage cheese
2 ripe bananas, mashed (about 3/4-1 cup)
2 tablespoons unsweetened greek yogurt
2 eggs
3 tablespoons maple syrup
1 teaspoon vanilla extract
1/2 cup fresh or frozen blueberries
Instructions:
Preheat the oven to 350 degrees F. Line a muffin tin with liners or grease.
Combine the dry ingredients: Whisk the oat flour, whey protein, almond flour, baking powder, baking soda, cinnamon and salt in a large bowl.
Blend the cottage cheese using a handheld immersion blender, food processor or blender until smooth.
Mix the wet ingredients: In a separate bowl, whisk the banana, blended cottage cheese, greek yogurt, eggs, maple syrup and vanilla extract until smooth.
Combine the wet and dry ingredients in one bowl. Avoid over mixing.
Fold in the blueberries. Save a few for topping.
Fill each muffin tin about 3/4 of the way full. Top with a couple extra blueberries per muffin.
Bake for 22-25 minutes or until a toothpick comes out clean and the top looks lightly golden.
Cool for 5 minutes before transferring to a wire rack.
Store in the fridge for up to 5 days or in the freezer for up to 3 months.
Notes:
Pre-blending the cottage cheese helps prevent clumps in the muffins. It also makes it more fluffy, so you won't want to skip this step!
If on a fat loss journey, make sure to pair these muffins with a high protein meal. As a Nutritionist, I find sticking to meals without snacks provides the best fat loss results.
Nutrition Information Per Muffin:
10 grams protein | 17 grams carbs | 2 grams fiber | 3 grams fat | 139 calories

Studies Mentioned:
These look good! I'm looking forward to trying this recipe out. 😀
I'm allergic to all nuts except coconut. Can I use sprouted wheat flour? Thanks!