These high-protein pumpkin muffins are moist and decadent. They’re easy to make and come together in one bowl, making for easy cleanup!

It’s pumpkin season, and with the kids back at school, I love having these high-protein pumpkin muffins on hand for an easy breakfast option!
These muffins are easy to make, rich in pumpkin flavor, gluten-free, and come packed with 10g of protein per muffin.
High Protein Pumpkin Muffins with Cottage Cheese
For this recipe, you will need pumpkin puree, cottage cheese, eggs, vanilla, sugar, gluten-free flour blend, vanilla protein powder, pumpkin pie spice, baking soda, salt, and optional mini chocolate chips.
Step one: Mix the wet ingredients in a large bowl. Mix until smooth.
Step two: Add the dry ingredients into the bowl and mix until thoroughly combined.
Step three: Pour the batter into prepared muffin tins, filling 2/3 full. Place the muffin pan in the oven and bake for 30 minutes or until golden brown.
Allow the muffins to cool to room temperature before serving. Store the muffins in an airtight container for up to a week. Freeze in a freezer-safe container for up to three months.

Tips & Substitutions
- Blend the Cottage Cheese: You can blend the cottage cheese first before using in this recipe. This will help with the cheese not being chuncky in the recipe. This is not a necessary step, but it is helpful for those who want to avoid this issue.
- Sugar: Use any granulated sugar you like. I like to use coconut and brown sugar, but sugar-free alternatives like monk fruit are great.
- Flour: Use all-purpose flour or gluten-free flour blend in this recipe. I like to use Bob’s 1:1 gluten-free flour blend in my baking.
- Protein Powder: I used a plant-based protein powder, but you can use whey powder instead. I suggest using vanilla-flavored protein powder.
- Chocolate Chips: This is an optional ingredient and can be omitted. You may add other ingredients like walnuts or dried fruit instead if you like.
Watch The Recipe Video
Protein Pumpkin Muffins FAQ
Can I substitute the cottage cheese?
If you’re not a fan of cottage cheese, you can substitute it with Greek yogurt or plant-based yogurt for a dairy-free option. Blending the cottage cheese beforehand helps smooth out its texture if you’re concerned about chunks.
Can I use regular flour instead of gluten-free flour?
Yes, you can use regular all-purpose flour or whole wheat flour if you don’t need the recipe to be gluten-free. If you doneed a gluten-free option, I recommend using a 1:1 gluten-free flour blend, like Bob’s Red Mill.
What type of protein powder should I use?
You can use any protein powder you prefer. Vanilla-flavored protein powder works best for this recipe, but you can experiment with other flavors as well. Both plant-based and whey protein powders will work.
Do I have to add chocolate chips?
No, chocolate chips are optional. You can leave them out or substitute them with other mix-ins like walnuts, pecans, or dried fruit for a healthier twist.
Can I use a sugar substitute?
Yes, you can use sugar-free alternatives like monk fruit sweetener, erythritol, or stevia if you want to reduce the sugar content. Coconut sugar or brown sugar are great natural options as well.
How long do these muffins last?
You can store the muffins in an airtight container at room temperature for up to a week. For longer storage, freeze them in a freezer-safe container for up to 3 months.

Related Recipes:
- Harvest Pumpkin Cookies (with Almond Flour)
- Pumpkin Muffins (with Almond Flour!)
- Perfect Pumpkin Pancakes (with Almond Flour)
- Pumpkin Muffins with Coconut Flour

High Protein Pumpkin Muffins with Cottage Cheese
These high-protein pumpkin muffins make an excellent breakfast for busy mornings!
- Prep Time: 10 minutes
- Cook Time: 30 minutes
- Total Time: 40-45 minutes
- Yield: 12 muffins 1x
- Category: Baked Goods
- Method: Oven
- Cuisine: American
Ingredients
- 1 cup pumpkin puree
- 1/2 cup cottage cheese
- 3 large eggs
- 1 teaspoon vanilla extract
- 1/3 cup granulated sugar (coconut sugar or brown sugar)
- 1 1/2 cups gluten-free flour blend
- 1/2 cup vanilla protein powder
- 2 teaspoons pumpkin pie spice
- 2 teaspoons baking powder
- 1/4 teaspoon salt
- 1/2 cup mini chocolate chips (optional)
Instructions
- Preheat the oven to 350°F.
- Grease and line a muffin pan.
- Optional: Blend the cottage cheese in a blender before adding to the mixture.
- Mix the pumpkin, eggs, cottage cheese, and vanilla in a large bowl until smooth.
- Add the flour, protein powder, sugar, baking powder, salt, pumpkin pie spice, and chocolate chips. Mix until thoroughly combined.
- Pour the batter into the lined muffin tins.
- Bake in the oven for about 30-35 minutes, or until the top of the muffins begin to brown.
- Remove the muffins from the oven and cool at room temperture before serving.
Nutrition Facts
- Serving Size: 1 muffin
- Protein: 10g



