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Home » Recipes » Muffins

Cottage Cheese Pumpkin Muffins

By Laura Fuentes Updated Apr 13, 2026

5 from 2 votes

Recipe

This post may contain affiliate links. Read our disclosure policy here.

Pumpkin cottage cheese muffins are super moist, full of fall flavor, and made with a boost of protein you can feel good about.

These pumpkin muffins with cottage cheese are easy to make and have everything you love from the classic muffin.

six cottage cheese pumpkin muffins

Pumpkin Muffins with Cottage Cheese

The internet (and me!) has been on a cottage cheese roll, adding it to everything from pancakes to muffins. In testing these pumpkin cottage cheese muffins, I found that I really like the added moisture they gave to my pumpkin spice muffins.

While these aren't quite as healthy as my banana cottage cheese muffins, the added protein makes me feel better about going back for seconds. 

Ingredients 

These muffins call for classic baking ingredients: butter, eggs, vanilla extract, all-purpose flour, sugar, and baking powder. For extra protein, moisture, and fall flavor, you’ll also add cottage cheese, pumpkin puree, and pumpkin spice (you can swap it for cinnamon).

How to Make Cottage Cheese Pumpkin Muffins 

These pumpkin muffins come together following these steps:

  1. Prep
    Before you start cooking, you want to preheat the oven and grease or line your muffin pan.
  2. Make the batter
    Blend the wet ingredients in the blender until smooth. In a large bowl, mix the dry ingredients. Then, pour the liquid mixture into the dry ingredients. If you want to add chopped nuts, now is when you fold them into the batter.
  3. Bake
    Fill the prepared muffin tin ¾ of the way to the top with batter and bake for 22 to 25 minutes until the tops have browned.

How Much Protein Per Muffin 

Cottage cheese gives these pumpkin muffins a protein boost, with 5 grams of protein per muffin.

More Cottage Cheese Breakfast Faves

Another fall favorite in my house is these cottage cheese pumpkin pancakes. So good! My kids also love it when I bake these blueberry cottage cheese muffins and this high-protein banana bread. And cottage cheese waffles? You’ll crave them often!

Cottage Cheese Pumpkin Muffins

a tray with six pumpkin cottage cheese muffins
Servings: 12 muffins
Prep Time: 5 minutes mins
Cook Time: 25 minutes mins
Total Time: 30 minutes mins
Pumpkin cottage cheese muffins are super moist, full of fall flavor, and made with a boost of protein you can feel good about.
5 from 2 votes
Print Pin

Ingredients

  • 1 cup cottage cheese
  • ½ cup pumpkin puree
  • ⅓ cup (6 tablespoons) melted butter, cooled
  • 2 large eggs
  • 1 teaspoon vanilla extract
  • 1 ¾ cup all-purpose flour
  • ⅓ cup sugar
  • 1 tablespoon baking powder
  • ¼ teaspoon salt
  • 1 teaspoon pumpkin spice*

Instructions

Prep:

  • Preheat the oven to 375F with the top oven rack positioned in the middle of the oven. Prep a 12-muffin pan with paper liners or generously grease it. If using silicone muffin liners, grease them with spray.

Make the batter:

  • In a blender, blend the cottage cheese, pumpkin puree, the melted butter cooled butter, eggs, and vanilla extract until smooth.
  • In a large bowl, mix the flour, sugar, baking powder, salt, and pumpkin spice.
  • Pour the liquid mixture into the large bowl and use a spatula to mix the batter until there's little to no visible flour left. If you want to add ½ cup chopped walnuts or pecans, fold them into the batter now.
  • Fill the prepared muffin tin ¾ of the way to the top with batter, then top them off with any remaining batter.

Bake:

  • Bake in the preheated oven for 22 to 25 minutes, until the tops have browned and a toothpick inserted in the middle comes out clean. Remove them from the oven and let them cool down.

Store:

  • Once cooled, store them in an airtight container at room temperature (on the counter) for 2 days, in the fridge for up to a week, and frozen for up to 3 months. I recommend warming them up in the microwave for 15 seconds before enjoying them.

Notes

  • Swap the pumpkin spice for 1 ½ teaspoons cinnamon. 

Equipment

¼ cup muffin batter scoop
Muffin Scoop
small jar of aluminum free baking powder
Aluminum-free baking powder
Muffin Pan
Clean Treats
Clean Treats Cookbook

Nutrition

Serving: 1 muffin | Calories: 163kcal | Carbohydrates: 21g | Protein: 5g | Fat: 6g | Saturated Fat: 4g | Polyunsaturated Fat: 0.4g | Monounsaturated Fat: 2g | Trans Fat: 0.2g | Cholesterol: 42mg | Sodium: 283mg | Potassium: 70mg | Fiber: 1g | Sugar: 7g | Vitamin A: 1794IU | Vitamin C: 0.5mg | Calcium: 83mg | Iron: 1mg

More Muffins

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    Mixed Berry Muffins
  • top view of lemon blueberry muffins
    Lemon Blueberry Muffins
  • top view of seven Greek yogurt banana muffins
    Greek Yogurt Banana Muffins
  • top view of seven banana blueberry muffins
    Banana Blueberry Muffins

Comments

    5 from 2 votes

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    Recipe Rating




  1. Linda says

    November 14, 2025 at 8:59 am

    5 stars
    These protein pumpkin muffins with cottage cheese were great! They were fluffy, moist and had great flavor!

    Reply
  2. Ivy says

    October 20, 2025 at 11:33 am

    5 stars
    I love pumpkin muffins! Such a great idea to add cottage cheese to the recipe!

    Reply
Laura fuentes holding a skillet of food standing in front of a blue door

Hi! I'm Laura.
Certified Integrative Nutrition Health Coach, mom of three, and the woman behind the world’s best pancakes—here to help you ditch the mealtime drama with recipes your family will actually eat.

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