Cottage Cheese Pumpkin Muffins are moist, bursting with fall flavor and 8 grams of protein, with chocolate chips inside and a crunchy pumpkin seed topping!
For the loaf version, check out my cottage cheese pumpkin bread.

Why You’ll Love This Recipe

As we move into fall, these cottage cheese pumpkin muffins are my newest of all my cottage cheese recipes! I do love adding cottage cheese to muffins because it sneaks in extra protein and keeps them moist without relying on much oil or butter.
I’ve already shared my cottage cheese muffins with chocolate chips and cottage cheese blueberry muffins, but I wanted a fall version.
For this cottage cheese pumpkin muffins recipe, I recommend blending the cottage cheese first. I usually skip that step, but here it makes the texture so much smoother. I found the curds dried up by day 2-3 and were a bit unpleasant to eat.
Ingredients for Cottage Cheese Pumpkin Muffins

- Cottage cheese: High in protein and adds moisture. Any % percentage works.
- Egg: Adds structure, moisture, and richness.
- Pumpkin puree: Use store-bought or homemade pumpkin puree, just not pumpkin pie filling.
- Maple syrup or honey: A natural way to sweeten without refined sugar. Any liquid sweetener works, but avoid dry sugar because it will throw off the batter.
- Oil: You only need a small amount. I like using a mild oil, like avocado oil, to keep the muffins moist without adding strong flavors.
- Vanilla extract: I use pure vanilla for the best flavor.
- Spices: Pumpkin pie spice and a little cinnamon for that cozy, warm fall flavor.
- Baking powder and baking soda: For a light, fluffy rise.
- All-purpose flour: For structure and tenderness. See Variations if you’re using whole wheat flour or gluten-free flour.
- Mini chocolate chips: Little pockets of melty chocolate that make every bite a treat. I love using mini chips so they distribute evenly throughout the muffins, but feel free to use the regular size or dark chocolate chips.
- Pumpkin seeds: I loved the crunchy, nutty topping, but feel free to skip it if you prefer.
How to Make Cottage Cheese Pumpkin Muffins

- Blend cottage cheese: Toss the egg and cottage cheese in a blender and blend until smooth. Egg just adds liquid to make it all move around.
- Make the batter: Pour mixture into a large bowl and add pumpkin puree, maple syrup, oil, vanilla, spices, baking powder, and baking soda. Whisk until smooth with no white lumps. Gently stir in the flour just until combined.
- Assemble the muffins: Fold in the chocolate chips, spoon the batter into the 12 cups of a muffin pan and sprinkle with pumpkin seeds.
- Bake and cool: Bake at 375 F for about 22 minutes, or until a toothpick comes out clean. Let the muffins sit for about 15 minutes and enjoy!
Tips for Best Results
Here are a few tips to make the best pumpkin muffins with cottage cheese.
- Blend the cottage cheese: Unless you buy small curd cottage cheese. Blending helps create a smoother, more pleasant texture in your muffins.
- Don’t overmix the batter: Stir just until the flour is incorporated, overmixing can make the muffins dense.
- Don’t over bake: Oven times can vary. A toothpick should come out clean but the muffins should still be soft.
- Pumpkin pie spice substitute: You can make your own pumpkin spice in 5 minutes by combining cinnamon, nutmeg, ginger and cloves. It tastes so much fresher and the pumpkin flavor is more vibrant than store-bought!

Variations
- Omit chocolate chips: Pumpkin cottage cheese muffins are just as delicious without chocolate. The pumpkin and spices will shine!
- Add nuts: Up to 1/2 cup chopped walnuts, pecans, or almonds.
- Whole wheat flour: You can swap in 1 1/2 cups of whole wheat or spelt flour.
- Gluten-free flours: They all behave a bit differently, so feel free to experiment. Try to swap 1:1 with white flour. If using oat flour, try about 2 1/3 cups. Almond flour or coconut flour won’t work.
- Add more protein: You will need to add some milk because protein powder dries out the batter. I would start with 1 scoop and go from there.
How to Store and Reheat
Store: Keep your muffins in a resealable bag or airtight container on the counter for up to 3 days.
Freeze: Transfer them to an airtight container and keep them in the freezer for up to 3 months.
Reheat: Just warm one up in the microwave for 20-30 seconds.
More Pumpkin Recipes to Try
- Pumpkin cottage cheese scones
- Healthy pumpkin muffins
- Pumpkin banana muffins
- Almond flour pumpkin muffins


Cottage Cheese Pumpkin Muffins
Equipment
Video
Ingredients
- 1 large egg
- 1 cup cottage cheese
- 1 cup pumpkin puree, not pumpkin pie filling
- 1/2 cup maple syrup or honey
- 3 tablespoons any mild oil, I used avocado oil
- 1 teaspoon pure vanilla extract
- 1 tablespoon pumpkin pie spice
- 1 teaspoon cinnamon
- 1/2 teaspoon baking powder
- 1/2 teaspoon baking soda
- 2 cups all-purpose flour
- 1/2 cup mini chocolate chips
- 1/4 cup pumpkin seeds
- Cooking spray, I use Misto
Instructions
- Preheat oven to 375 degrees F. Line muffin tin with muffin liners and spray with cooking spray. Set aside.
- In a blender, add egg and cottage cheese, blend until smooth.
- Pour into a large mixing bowl and add pumpkin puree, maple syrup, oil, vanilla extract, pumpkin pie spice, cinnamon, baking powder and baking soda. Whisk well until no white lumps of baking powder are visible.
- Add flour and gently mix just until combined. Add chocolate chips and give a few stirs to incorporate.
- Divide batter evenly between 12 openings of previously prepared muffin tin and sprinkle with pumpkin seeds. Bake muffins for 22-23 minutes or until toothpick inserted in the center comes out clean.
- Remove from the oven, let cool for 15 minutes and enjoy!
Notes
- Store: To prevent muffins from drying out, place in a resealable bag or airtight container and store on a counter for 2-3 days.
- Freeze: In an airtight container for up to 3 months.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.














These are probably the best pumpkin muffins I’ve ever made. I substituted apple sauce for the oil and it worked wonderfully. Thanks Olena for another delicious recipe! 😊
My pleasure, Kat!
Turned out great! I used the whole wheat flour option.
Wonderful, happy to hear!
I would like to make many of your recipes, but I we don’t like maple syrup nor honey. Is there a way to make them using xylitol? Should I increase the cottage cheese to 1,5 cups ?
I wouldn’t recommend it. I do think you will need to make more adjustments. Unfortunately I don’t think my recipes will work with dry sweetener. It has to be liquid one.
I love your recipes. Can’t wait to try these. Will leave a review when I do. Such delicious easy recipes you share with us. Thank you Olena.
My pleasure. Enjoy!