These cottage cheese muffins are soft, moist and packed with chocolate flavor and melty chocolate chips. They can’t be beat for an afternoon snack or a decadent, but healthy start to the day.
It’s mid-way through 2025 and I’m still loving the cottage cheese trend. These muffins are the latest in my quest to put it in everything for a higher protein outcome and a soft, fluffy result. If you haven’t yet tried cottage cheese bagels or cottage cheese pancakes, they should be next on your to-bake list.
Muffins are a natural next step for incorporating cottage cheese. Much like adding yogurt to some muffin batters, cottage cheese can be worked in just as easily. The outcome is a lighter, fluffier and super moist muffin that tastes like dessert thanks to chocolate protein powder and chocolate chips.
I love making a batch of these for the week and can find a way to enjoy them almost any time of day. They make just as good of a breakfast as they do a pre or post workout snack and can easily pass as dessert too. My recent favorite is crumbling one on top of my nightly Ninja creami concoction with a drizzle of peanut butter or homemade macadamia nut butter.
Why You’ll Love These
- Simple ingredients
- 5g of protein per muffin — thanks to cottage cheese and protein powder
- Easily made gluten-free
- Perfect for any meal of the day
Ingredient Highlights
- Flour — The recipe uses all-purpose flour but you can swap this out for your favorite gluten-free flour blend if desired. I’ve made these with King Arthur measure-for-measure and they come out great.
- Cottage cheese — You can grab low-fat or full-fat cottage cheese, it doesn’t make much of a difference in the recipe. Also, because the cottage cheese is blended before mixing with the other ingredients, the size of the curd doesn’t matter as much.
- Protein powder — Choose your favorite chocolate protein powder that bakes well. I’ve had success with Nuzest for a plant-based option and both Equip and Paleovalley for animal-based beef proteins. I don’t bake with whey any more but I’m sure that would work just as well.
- Sweeteners — I’ve scaled down the sweeteners by using less maple syrup (my choice over honey, but you can use either) and the recipe still works. Adjust within reason from a quantity perspective (I don’t recommend lowering by more than 2 tablespoons) and you can cater to your desired sweetness level.
- Milk — Any kind of milk will work — dairy or plant-based.
Step by Step Instructions
- Combine the blended cottage cheese, eggs, sugar, maple syrup and oil in a bowl and whisk until smooth.
- Add the flour, protein powder, baking powder, baking soda and salt and stir until combined.
- Stir in the milk until fully incorporated into the batter.
- Gently fold in the chocolate chips.
- Scoop the batter into a muffin tin lined with paper cups. Top each muffin with a few more chocolate chips.
- Bake in a 350°F preheated oven for 25-30 minutes until a toothpick inserted into the middle of a muffin comes out clean. Remove from the oven and let cool for a few minutes before transferring each muffin to a wire rack.
My Pro Tip
Best Tip For Success
*Don’t over-mix the batter if you want a light and fluffy muffin. Over-mixing results in a dense final result. Less is always more when incorporating ingredients.
Variations
Here are a few ways you can play around with the cottage cheese muffins and enjoy different flavors and textures.
- Change the protein powder to another flavor like vanilla and swap out the chocolate chips for fruit like blueberries and lemon zest (like these oatmeal muffins) or another berry.
- Add some chopped nuts such as walnuts, peanuts or hazelnuts.
- Add 1-2 tablespoons of cacao powder for extra-chocolatey muffins.
Storage
Make sure to let the muffins cool completely once they’re baked. They can then be stored in an airtight silicone bag, plastic bag or container for a few days at room temperature. If it’s hot in your house, place them in the refrigerator.
If you want to freeze the muffins, arrange them on a plate or baking sheet and freeze individually before transferring to a freezer-safe bag or container. They’ll keep for up to 3 months in the freezer and can be thawed in the refrigerator in just a few hours.
More Healthy Muffins
- Banana zucchini muffins
- Sweet potato bran muffins
- Peanut butter banana muffins
- Chocolate chip avocado muffins
Chocolate Cottage Cheese Muffins
Ingredients
- 1 ½ cups all-purpose flour
- 1 scoop chocolate protein powder, *see notes
- ½ cup coconut sugar
- 2 eggs
- 1 cup cottage cheese
- ⅓ cup melted coconut oil
- ⅓ cup honey or maple syrup
- 1 ½ teaspoons baking powder
- ½ teaspoon baking soda
- ½ teaspoon salt
- ½ cup chocolate chips
- ½ cup milk, any kind of milk will work
Instructions
- Preheat the oven to 350°F and line a muffin tin with paper liners or lightly grease it.
- Blend the cottage cheese in a blender or food processor until smooth and creamy. This step helps create a soft, uniform muffin texture.
- In a large bowl, whisk together the blended cottage cheese, eggs, coconut sugar, honey (or maple syrup) and oil until smooth and fully combined.
- Add the dry ingredients: flour, protein powder, baking powder, baking soda and salt. Gently fold the mixture using a spatula until just combined. Do not over-mix.
- Stir in the milk and mix until fully incorporated.
- Add the chocolate chips and gently fold them into the batter.
- Divide the batter evenly into the muffin cups, filling each to the top. Sprinkle extra chocolate chips on top if desired.
- Bake for approximately 25-30 minutes, or until a toothpick inserted in the center comes out clean or with just a few moist crumbs.
- Remove from the oven and let cool on a wire rack before serving.
Notes
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Gina Matsoukas is an AP syndicated writer. She is the founder, photographer and recipe developer of Running to the Kitchen — a food website focused on providing healthy, wholesome recipes using fresh and seasonal ingredients. Her work has been featured in numerous media outlets both digital and print, including MSN, Huffington post, Buzzfeed, Women’s Health and Food Network.
I do not like coconut – what would I use to replace coconut oil and coconut sugar?
Thank you!
The coconut oil can be substituted with another oil like avocado or even butter. Coconut sugar can be swapped with brown sugar.
What to use instead of a protein powder? Could I just use extra “flour”?
Thanks!
Yes, that will work fine. You’ll probably need about 1/4 cup extra.
How much is the “scoop” of protein powder? Is it 1/4 cup, 1/3 cup? Different brands use different size scoops.
The difference between 1/3 cup, 1/4 cup, etc for a protein powder scoop won’t matter in the recipe, that’s why I didn’t specify. Just use 1 scoop of your favorite protein powder. I find most are about 1/4 cup.