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Home » Muffins

Published on October 1, 2026. Published by Megan

Cottage Cheese Pumpkin Muffins

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Fluffy cottage cheese pumpkin muffins scattered to show the domed tops with chocolate chips and pumpkin seeds.

Cottage cheese pumpkin muffins are soft, moist, fluffy and perfectly spiced pumpkin muffins filled with protein. Cottage cheese creates a creamy tender   texture that blends perfectly into these protein pumpkin muffins. They’re perfect for an easy fall breakfast, snack, or healthier pumpkin treat you’ll want to make all season long.

Jump to:
  • Why Make This Recipe
  • Ingredients and Substitutions
  • How To Make 
  • How To  Store, Freeze and Thaw 
  • M’s Expert Tips
  • FAQs
  • Other Pumpkin Muffins Recipes to Try
  • Cottage Cheese Pumpkin Muffins Recipe

Why Make This Recipe

I love adding an extra boost of protein to some of my easy to make recipes. Cottage cheese is such an easy way to add more protein to almost anything and no, you can’t even taste it. My Cottage Cheese Brownies, Cottage Cheese Blueberry Muffins, Cottage Cheese Banana Bread, Cottage Cheese Pancakes, Cottage Cheese Cookie Dough and Cottage Cheese Chocolate Mousse  are some of my favorite cottage cheese recipes on the blog. These cottage cheese pumpkin muffins are no exception and I know you will love them too. 

  • Layers of flavors and textures. This recipe for pumpkin muffins with cottage cheese has a perfectly moist and soft texture filled with all the cozy warming spices you love about pumpkin muffins. You can’t even taste the cottage cheese. 
  • Easy to make, bake and eat.These soft, fluffy and tender pumpkin muffins with cottage cheese is just as simple to make as classic pumpkin muffins. The only difference is adding in 1 -2 extra minutes to blend the cottage cheese. 
  • You love healthier for you sweet treats. Who doesn’t love a healthier twist on already delicious pumpkin muffins? The addition of cottage cheese adds a boost or protein and moisture, the warming spices all flavor and a boost of vitamins and mineral. Top with pumpkin seeds for a healthy, crunchy topping.

Ingredients and Substitutions

These soft and fluffy cottage cheese pumpkin muffins require only a handful of simple ingredients to make and you probably already have them in your pantry and fridge. 

Ingredients to make pumpkin cottage cheese muffins in bowls.
  • All Purpose Flour: To make this pumpkin cottage cheese muffin recipe gluten free, use a good 1-1 gluten free flour. I recommend using the one from Bob’s Red Mill. Make sure to measure the flour by grams (240 g) versus cup for cup for the most accurate substitution. 
  • Baking Powder: This recipe hasn’t been tested with baking soda. Double check to make sure the baking soda is in date.  
  • Ground Spices: I love a lot of sweet warming spices when I bake with pumpkin. If you don’t have all the ground spiced on hand, you can also use 4 teaspoons pumpkin spice,  chai spice or apple pie spice blends.
  • Canned Pumpkin Puree: You can use the same amount of fresh pumpkin puree if you have some on hand. Do not use pumpkin pie filling. 
  • Cottage Cheese: Use a cottage cheese you love. The flavor will not to prominent in the muffins. Blending the cottage cheese will smooth out the curds, so just use the kind you love. I personally love using one that is 4% fat. The cottage cheese from Good Culture or Daisy Cottage Cheese are both good choices. 
  • Unsalted Butter and Oil: Feel free to use your preferred unsalted butter and preferred neutral baking oil such as vegetable, canola, avocado or olive oil. If you want, feel free to use all butter or all oil. 
  • Sugar and Light Brown Sugar: This recipe hasn’t been tested with alternative sugars. However, maple sugar would be a good substitute to make these pumpkin muffins with cottage cheese refined sugar free. 
  • Eggs: This recipe hasn’t been tested without eggs. 
  • Vanilla Extract: This provides a lovely background flavor for the spices, pumpkin and cottage cheese.

How To Make 

Learn how to make cottage cheese pumpkin muffins in a few easy steps.

  1. Preheat the oven to 400 F (205 C). Line (2) 12 ct. muffin pans with cupcake liners. Add the cottage cheese to a blender or food processor. Blend or process until the cottage cheese is smooth like yogurt or cream cheese. Add the cottage cheese to a large mixing bowl. Whisk in the pumpkin puree, oil or melted butter, sugar, light brown sugar, eggs and vanilla extract until smooth and well combined. 
  2. In another mixing bowl, whisk the flour, baking powder, ground spices and salt together until well combined. Whisk in the dry ingredients until just combined.
  1. Use a 3 tablespoon sized cookie scoop to scoop the cottage cheese pumpkin muffin batter into each of the muffin liners, alternating every other cup. Top with pumpkin seeds and chocolate chips if you like. 
  2. Bake the pumpkin cottage cheese muffins at 400 for 18 - 20 minutes. The muffins are done when a toothpick inserted into the center comes about with a few moist crumbs or when a finger pressed gently into the center of the muffins quickly bounces back. Cool the pumpkin cottage cheese muffins in the muffin pan for 5 - 10 minutes. Carefully remove the muffins to cool to room temperature and enjoy!

How To  Store, Freeze and Thaw 

  • Store: Due to the high moisture and dairy content of these muffins, it is best to store them in the fridge after 1 day. For longer storage, I recommend storing them in the freezer. 
  • Freeze: Transfer each way or parchment wrapped muffin into a ziplock bag. Store in the freezer for up to 2 months. 
  • Thaw: The easiest and best way to thaw the protein pumpkin muffins is to let them slowly thaw in the fridge. Then pop one or two muffins into the microwave for that “fresh from the oven” taste.
Up close of bite taken out of the pumpkin cottage cheese muffin showing the fluffy interior.

M’s Expert Tips

  • Blend the cottage cheese. Unless you love the lumps that come from the curds, I suggest blending the cottage cheese until smooth and creamy, like yogurt or sour cream. 
  • Bring cold ingredients to room temperature. This allows the ingredients to mix together more evenly which requires less mixing, resulting in moist and perfectly mixed protein pumpkin muffins. 
  • Don’t overmix the batter. Make sure to mix the dry ingredients into the wet until just combined. 
  • Alternate muffin wells in the muffin pan. This allows each muffin to get the maximum of amount of even heat circulating around it. The tops will still pop up, but they won’t be as high if you decide to fill all the muffin liners at once.
  • Top with your preferred topping. I love a little crunch on top of my muffins. Top these protein muffins with pumpkin seeds, chocolate chips, spiced sugar or even streusel.

FAQs

Can I make this pumpkin cottage cheese muffins recipe as mini muffins?

You absolutely can! Prepare the muffins according to the recipe directions. Grease and line or simply grease a 24 count mini muffin pan really well. Add the batter to the muffin wells, top as you like. Bake a 375 F (190 C) for about 10 - 14 minutes or until the tops bounce back quickly.

What does cottage cheese do for muffins?

Cottage cheese adds an extra boost of protein, while making the muffins extra moist with a tender crumb.

Can I add cottage cheese to any muffin recipe?

It’s really easy to add cottage cheese to almost any muffin recipe. Simply blend the cottage cheese to make it smooth. Replace milk, buttermilk, yogurt or sour cream with an equal amount of blended cottage cheese.

Up close photo showing the soft, dome of the pumplin cottage cheese muffins topped with crunchy pumpkin seeds and melty chocolate chips.

Other Pumpkin Muffins Recipes to Try

  • Pumpkin Banana Muffins
  • Mini Pumpkin Muffins
  • Easy Pumpkin Muffins
  • Pumpkin Cream Cheese Muffins

If you try this Cottage Cheese Pumpkin Muffins recipe please rate the recipe and leave a comment below. Doing so helps other readers decide if this is a great recipe to bake. Don’t forget to tag me on Instagram using @olivesnthyme so I can see what you’re baking! Happy Baking! -M

Cottage Cheese Pumpkin Muffins Recipe

Megan
These cottage cheese pumpkin muffins are soft, tender, perfectly spiced and filled with creamy protein. They come together with simple ingredients and make an easy breakfast, snack, or afternoon treat. If you’re looking for a delicious high protein pumpkin muffin to enjoy all season long, this recipe is one to try.
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Prep Time 15 minutes mins
Cook Time 18 minutes mins
Cooling Time 10 minutes mins
Total Time 43 minutes mins
Course Breakfast, Snack
Cuisine American
Servings 12 muffins

Equipment

  • 1 food processor or blender
  • 1 - 2 12 ct muffin pans
  • 2 mixing bowls
  • 1 whisk
  • 1 large cookie scoop (3 tbsp, 45 ml) optional

Ingredients
  

Cottage Cheese Pumpkin Muffins

  • 1 cup (226 g) blended cottage cheese
  • 2 large eggs, room temperature
  • 1 cup (240 g) canned pumpkin puree
  • ½ cup (120 ml) oil or melted butter
  • ½ cup (100 g) light brown sugar
  • ½ cup (100 g) granulated sugar
  • 2 teaspoons (10 ml) vanilla extract
  • 2 cups (240 g) all purpose flour
  • 1 tablespoon baking powder
  • 2 teaspoons ground cinnamon
  • 1 teaspoon ground ginger
  • ¼ teaspoon nutmeg, cloves, all spice ¼ of each or use ¾ -1 teaspoon your preferred ground spice
  • ¼ teaspoon salt

Optional Toppings

  • ½ cup (85 g) chocolate chips
  • ½ cup pepitas (pumpkin seeds)

Instructions
 

  • Preheat the oven to 400 F (205 C). Line (2) 12 ct. muffin pans with cupcake liners. 
  • Add the cottage cheese to a blender or food processor. Blend or process until the cottage cheese is smooth like yogurt or cream cheese. 
    Add the cottage cheese to a large mixing bowl. Whisk in the pumpkin puree, oil or melted butter, sugar, light brown sugar, eggs and vanilla extract until smooth and well combined. 
    1 cup (226 g) blended cottage cheese, 2 large eggs, room temperature, 1 cup (240 g) canned pumpkin puree, ½ cup (120 ml) oil or melted butter, ½ cup (100 g) light brown sugar, ½ cup (100 g) granulated sugar, 2 teaspoons (10 ml) vanilla extract
  • In another mixing bowl, whisk the flour, baking powder, ground spices and salt together until well combined. Whisk in the dry ingredients until just combined.
    2 cups (240 g) all purpose flour, 1 tablespoon baking powder, 2 teaspoons ground cinnamon , 1 teaspoon ground ginger, ¼ teaspoon nutmeg, cloves, all spice , ¼ teaspoon salt
  • Use a 3 tablespoon sized cookie scoop to scoop the cottage cheese pumpkin muffin batter into each of the muffin liners, alternating every other cup.
    Top with pumpkin seeds and chocolate chips if you like. 
    ½ cup (85 g) chocolate chips, ½ cup pepitas (pumpkin seeds)
  • Bake the pumpkin cottage cheese muffins at 400 for 18 - 20 minutes. The muffins are done when a toothpick inserted into the center comes about with a few moist crumbs or when a finger pressed gently into the center of the muffins quickly bounces back.
    Cool the pumpkin cottage cheese muffins in the muffin pan for 5 - 10 minutes. Carefully remove the muffins to cool to room temperature and enjoy.

Notes

Store: Due to the high moisture and dairy content of these muffins, it is best to store them in the fridge after 1 day. For longer storage, I recommend storing them in the freezer. 
Cottage Cheese Pumpkin Muffins Troubleshooting Checklist
  • Dense muffins? Don’t overmix the batter, and measure flour carefully.
  • Dry muffins? Check them early and avoid overbaking.
  • Wet centers? Bake a little longer, covering loosely with foil if the tops brown too quickly.
  • Visible cottage cheese? Blend the cottage cheese until completely smooth before adding it.
  • Muffins didn’t rise? Make sure your leavening agents are fresh and measured correctly.
  • Sticking to the pan? Grease the pan well or use muffin liners, then let muffins cool for a few minutes before removing.
Keyword Cottage Cheese Pumpkin Muffins, Cottage Cheese Pumpkin Muffins Recipe, fall baking, Protein Pumpkin Muffins, Pumpkin Recipes
did you make this recipe?tag @olivesnthyme on Instagram

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Hi friends, I'm Megan!

Welcome to my blog, Olives + Thyme. I am a food photographer and blogger with a love of all things sweet.

Here you'll find mostly sweet recipes that are simple to make and full of flavor.

Learn more about me

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