Chocolate Cottage Cheese Muffins

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. It’d also be great crumbled over this cottage cheese ice cream, especially since that one already has peanut butter and chocolate worked into it.

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

1. 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.
2. 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.
3. 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.
4. 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.
5. Milk — Any kind of milk will work — dairy or plant-based.

Step by Step Instructions

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