Cottage Cheese Pumpkin Muffins
These easy Cottage Cheese Pumpkin Muffins are packed with protein and flavor. They are perfect this time of year, and are made using simple ingredients you probably already have at home. Enjoy your fall season with these low-carb, high-protein muffins.

Pumpkin cottage cheese muffins are the in thing this fall. They are a perfect grab-and-go breakfast or snack. You can even add some icing on top and change them into cupcakes.
It’s such an easy recipe that you can have for all your daily breakfasts, without feeling any guilt. Now is the perfect time to make this healthy muffin recipe!
Speaking of cottage cheese recipes, be sure to try these Cottage Cheese Crepes and this Whipped Cottage Cheese Dessert as two of my other top picks.

Ingredients
- Almond flour – Adds a nice depth of flavor to the muffins.
- Coconut flour – Adds a nice coconut flavor.
- Joy Filled Eats sweetener – My go-to sweetener for low carb recipes.
- Cinnamon or pumpkin spice – Either option works.
- Baking powder – Gives the muffins a fluffy texture.
- Pumpkin puree – Don’t confuse this with pumpkin pie filling (which has added sugar).
- Coconut oil – Helps add a healthy fat to the muffins.
- Cottage cheese – All cottage cheese brands will work.
- Eggs – The binding agent for the dry ingredients.
- Vanilla extract – Adds a nice pop of vanilla flavor.
See the printable recipe card for quantities.

How to Make Cottage Cheese Pumpkin Muffins
Preheat the oven to 350 degrees. Add eight paper lines in a muffin tin. Spray them with cooking spray.

Step One: Add the dry ingredients to a mixing bowl and stir.

Step Two: Next, add the wet ingredients and mix. Don’t overmix. Stir until just incorporated.

Step Three: Scrape down the sides of the bowl. The batter will be thick.

Step Four: Divide the muffin batter between the eight prepared liners.

Step Five: Place the muffin pan in the oven and bake for 45-55 minutes or until they are no longer jiggly and the edges are golden brown. Cover with foil, if needed.

Step Six: Cool in the pans for 10 minutes and then transfer to a wire rack. Enjoy!
Top Tip💡
These do take a long time to bake. And ovens can vary a lot. You want to bake until they are no longer jiggly. If needed, cover the top with aluminum foil so it doesn’t get too dark.
Variations
- Protein powder – Adding protein powder in place of the coconut flour ups the protein power even more. Adding vanilla protein powder would be a good flavor choice for pumpkin protein muffins but you may want to reduce the sweetener.
- Dark chocolate chips – Everyone loves the flavor combo of pumpkin and chocolate! You could use semi-sweet chocolate chips or white chocolate chips as well.
See this Keto Pumpkin Bread for another one of my favorite low carb fall recipes!

Equipment
You don’t need a ton of equipment to make these low-carb pumpkin muffins. A hand mixer, a large mixing bowl, paper towels, and a muffin pan are really all you need!
Storage
Once you make a batch of these muffins, all you have to do is let them cool to room temperature and store them in an airtight container. Plan on keeping them in the fridge to stay fresh.
You can also freeze these muffins to enjoy later.

Common Questions
You can add any toppings that you want! Just keep in mind that any additional ingredients that you add will change the carb and nutritional value.
Some topping ideas could be a drizzle of cream cheese frosting, a dusting of powdered sugar, or even a little bit of cinnamon sugar right on top.
You may have overstirred the muffins. Keep in mind that you should stir just until the wet ingredients and dry ingredients are combined.
I always do because of the added cottage cheese. With the dairy addition, it’s important to regulate the temperature.
If you’re not a fan of eating cold muffins, you can always take them out of the fridge and let them come to room temperature or warm them in the microwave for a short amount of time.
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Cottage Cheese Pumpkin Muffins
Ingredients
- 3/4 cup almond flour
- 1/3 cup coconut flour
- 1/4 cup Joy Filled Eats Sweetener (or see alternatives in recipe notes)
- 1.5 tsp cinnamon or pumpkin spice
- 1 tsp baking powder
- 3/4 cup pumpkin puree
- 1/2 cup coconut oil melted
- 1/2 cup cottage cheese
- 3 eggs
- 1 tsp vanilla
Instructions
- Preheat oven to 350. Put 8 paper liners in a muffin pan and spray with cooking spray.
- Stir together the dry ingredients.
- Add the wet ingredients and mix just until they are incorporated.
- Divide the batter between the prepared muffin tin.
- Bake for 45-55 minutes or until no longer jiggly and golden around the edges.
Notes
Nutrition
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Hi! Seeing as these are baked, can I use avocado (or other neutral) oil instead of coconut oil?
Yes, any neutral oil should work.
Fantastic recipe, love them.
It will be my go to, especially for traveling. Thank you 😊
😋 LOOKS YUM 👏🏼👏🏼👍🏼😋DO YOU think This Can be Made into Mug CAKES? JUST wondering 😊Thanks for sharing ❤️ We Do Have Vanilla protein And Thank you FOR mentioning ABOUT cutting Back on The sugar IF you ADD it 👍🏼❤️❗️Appreciate it 😊G-d❤️Bless ❗️
I have not tried this as a mug cake. If you do please let me know how it turns out 🙂