Table of Contents
Cottage Cheese Muffins Recipe: Pumpkin & Chocolate Chip
As a busy mom of 3 trying to sneak some extra protein into our everyday meals, these Cottage Cheese Muffins have been a total game-changer! For the pumpkin version, the cozy pumpkin spice flavor is perfect for fall. The chocolate chip version tastes like a total treat, but I love that they’re also full of protein thanks to the cottage cheese. This surprising secret ingredient not only adds protein, but it makes the muffins super fluffy and delicious, too!
If you loved my Viral Cottage Cheese Pancakes recipe, then you’ll love this one! The muffins turn out soft, slightly sweet, and full of that cozy pumpkin spice or chocolate chip goodness we all crave. Plus, they can be made entirely in a blender in just 10 minutes and then just 30 minutes of baking time. So easy! They’re perfect for the entire family for breakfast, snacks, or even as a grab-and-go treat.
You’ll Also Love: Cottage Cheese Egg Muffins

Cottage Cheese Muffins Recipe Ingredients
The ingredients are simple, easy to find, and the best part: protein muffins without protein powder! Here’s what you’ll need:
Pumpkin Protein Muffins
- Cottage Cheese: Whole milk cottage cheese works best for that rich, creamy texture, but you can use low-fat if you prefer. It’s the secret ingredient that gives these muffins a protein boost and a super light and fluffy texture!
- Maple Syrup: Natural sweetness! I love using maple syrup because it pairs so well with pumpkin and keeps the muffins refined sugar-free. Agave syrup works great, too.
- Vanilla Extract
- Pumpkin Puree: Can’t have pumpkin muffins without pumpkin! Be sure to grab 100% pure pumpkin puree (not pumpkin pie filling). Feel free to substitute with an equal amount of mashed banana or applesauce instead!
- Eggs
- All-Purpose Flour: You can use regular or gluten-free all-purpose flour. Whole wheat flour also works great for added nutrition, but I would only substitute half of the all-purpose flour amount and use regular flour for the rest!
- Baking Powder/Salt
- Pumpkin Spice: The real star of the show! It brings in all the cozy fall flavors. Feel free to swap this with cinnamon or omit it completely for a more neutral flavor!
- Mini Chocolate Chips: Totally optional, but I love adding them for a little extra treat. Regular chocolate chips work great, too! My kids are big fans of the chocolatey bites in every muffin.

Chocolate Chip Protein Muffins Ingredients
Not feeling the pumpkin version of these cottage cheese muffins? Here’s what you’ll need to make regular chocolate chip ones:
- Cottage Cheese
- Maple Syrup
- Vanilla
- Eggs
- Applesauce
- Coconut Oil
- Baking Powder/Salt
- Mini Chocolate Chips

How to Make High Protein Muffins Without Protein Powder
These muffins are so easy to make, and everything comes together in just a few simple steps. You can make them entirely in a blender, or simply blend the liquid ingredients and then fold them into the dry ingredients. Either way works great! Here’s how to make Cottage Cheese Muffins:
- Blend the Wet Ingredients: Start by blending the cottage cheese, maple syrup, vanilla, pumpkin puree, and eggs (or all liquid ingredients for the non-pumpkin version). The blender makes everything smooth, so there’s no weird texture from the cottage cheese—just silky creamy goodness!
- Mix the Dry Ingredients: In a large bowl, combine the flour, baking powder, pumpkin spice, and salt and mix JUST until combined (be careful not to overmix the batter). Another option is to gently blend the dry ingredients with the wet!
- Combine: Pour the wet mixture into the dry ingredients and fold everything together. Then, stir in those chocolate chips if you’re using them.
- Bake: Spoon the batter into a lined muffin tin, and bake at 350°F for about 25-30 minutes. You’ll know they’re ready when a toothpick comes out clean. Let them cool slightly and enjoy!
RELATED: 45+ Healthy Pumpkin Recipes
Tips
- Use Whole Milk Cottage Cheese: I find that whole milk cottage cheese gives these muffins the best texture, but low-fat will work in a pinch.
- Don’t Overmix: When combining the wet and dry ingredients, fold everything together gently to keep the muffins nice and fluffy. While blending them works, mixing in a bowl results in a better texture!
- Pumpkin Spice Blend: If you’re out of pumpkin spice, you can make your own by mixing cinnamon, nutmeg, ginger, and a pinch of cloves.
- Chocolate Chip Options: Feel free to use regular chocolate chips or even dark chocolate if you want a slightly more indulgent flavor. White chocolate chips could be great with the pumpkin spice flavors, too!





Variations for Healthy Cottage Cheese Muffins
Banana Cottage Cheese Muffins – Swap the pumpkin puree for mashed ripe bananas. You’ll need about 1/2 cup of mashed banana to replace the pumpkin. The bananas add natural sweetness, so you can reduce the maple syrup slightly if you want. These are great for banana bread lovers!
Apple Cottage Cheese Muffins – Replace the pumpkin puree with unsweetened applesauce (1/2 cup works perfectly). You can also stir in some small cubes of fresh apple for extra texture and a bit of cinnamon for more fall flavor.
Blueberry Cottage Cheese Muffins – Swap the chocolate chips in the regular cottage cheese muffins recipe for fresh or frozen blueberries. It’s that easy!
Pumpkin Walnut Protein Muffins – Try adding nuts like walnuts or pecans for extra crunch, or even a handful of dried cranberries for a seasonal twist.
Gluten-Free Protein Muffins – Just sub the all-purpose flour with your favorite gluten-free all-purpose flour blend. I’ve tested this and they turn out great!

How to Store High Protein Muffins Without Protein Powder
Refrigerator: Store these cottage cheese muffins in an airtight container in the fridge for up to 4-5 days. To reheat, place them in the microwave for about 10-15 seconds to bring back that fresh-from-the-oven taste.
Freezer: These muffins also freeze really well! Let them cool completely, then store them in a freezer-safe bag or container for up to 3 months. When you’re ready to enjoy, just thaw them overnight in the fridge or pop them in the microwave for about 20-30 seconds until warm.
FAQ
Absolutely! These muffins are a great way to boost protein without using protein powder. The cottage cheese provides a hefty dose of protein, so you don’t need any extra supplements to make these muffins a healthy, protein-packed treat.
If you’re out of pumpkin or want to make these muffins at a different time of year, you can easily substitute them with mashed banana or applesauce. Both options will still give you that moist, soft texture. Just keep in mind the flavor will change a bit but in a good way!
Yes! Using whole milk cottage cheese can be a great substitution for oil in muffins. This gives the muffins more protein and a delicious flavor!

More Healthy Pumpkin Recipes
- Pumpkin Oatmeal Pancakes
- Healthy Pumpkin Bread
- Pumpkin Spice Creamer
- Gluten-Free Pumpkin Bars
- Pumpkin Spice Chai Latte
Healthy Muffin Recipes You’ll Love
- Blueberry Banana Protein Muffins
- Chocolate Zucchini Muffins
- The BEST Healthy Pumpkin Muffins
- Healthy Chocolate Chip Muffins
- Gluten-Free Lemon Raspberry Muffins
- Banana Chocolate Chip Oatmeal Muffins
More From Jar Of Lemons
Want to save this recipe? Enter your email below and I’ll send the recipe to your inbox. Plus you’ll get new healthy recipes every week!
Cottage Cheese Muffins
Equipment
Ingredients
Pumpkin Cottage Cheese Muffins
- 3/4 cup cottage cheese (whole milk works best)
- 1/3 cup maple syrup
- 1 teaspoon vanilla extract
- 1/3 cup pumpkin puree
- 2 large eggs
- 1 1/2 cup all-purpose flour (or gluten-free all-purpose flour)
- 1 1/2 teaspoons baking powder
- 2 teaspoons pumpkin spice
- 1/4 teaspoon salt
- 1/2 cup mini chocolate chips (or regular)
Chocolate Chip Cottage Cheese Muffins
- 3/4 cup cottage cheese (whole milk works best)
- 1/2 cup maple syrup
- 1 teaspoon vanilla extract
- 1/4 cup applesauce
- 2 Tablespoons coconut oil (melted and cooled)
- 2 large eggs
- 1 1/2 cup all-purpose flour (or gluten-free all-purpose flour)
- 1 1/2 teaspoons baking powder
- 1/4 teaspoon salt
- 1/2 cup mini chocolate chips (or regular)
Instructions
- Preheat the oven to 350 degrees F and line a muffin tin with liners.
- Combine the cottage cheese, maple syrup, vanilla, pumpkin puree, and eggs in a blender (or all liquid ingredients for the regular chocolate chip version).
- Blend until smooth.
- Mix it with the flour, baking powder, pumpkin spice, and salt in a large mixing bowl (or lightly blend in the dry ingredients).
- Fold in the chocolate chips.
- Spray the muffin liners with a little bit of oil and pour the batter into each one.
- Bake for 25-30 minutes.
- Let cool for a few minutes and enjoy!

Colleen says:
Made the chocolate chip muffins today turned out great very tasty followed recipe exactly except replaced 1/2 cup of gluten free flour for 1/2 cup almond flour.
Jar Of Lemons replied:
Thanks for the review, Colleen. I’m glad your substitution worked well for this muffin recipe!
Chelsry says:
Cont.. Oh and the cook time! 20 minutes was plenty for mine. I did 22 minutes and they were slightly over. I wish I had added the full amount of choc chips. I skimped thinking there would be a more pumpkin taste.
Chelsry says:
I would have loved a more deep pumpkin taste rather than the pumpkin spice taste. But they’re great otherwise.