Freezer-Friendly Pumpkin Cottage Cheese Muffins with Cream Cheese Frosting (GF)

If you know me, you know that I have never once turned down a pumpkin dessert. Pumpkin bread, pumpkin ice cream, pumpkin cheesecake, those giant frosted pumpkin cookies at the coffee shop, I want all of it the second the -ber months begin. This is exactly why I wanted to create these Pumpkin Cottage Cheese Muffins a reality. They taste like the pumpkin cake I actually want, but the whipped cottage cheese and optional scoop of cinnamon rolls protein powder work quietly in the background so I feel full afterward instead of standing in front of the panty. Almond and cassava flour keep them gluten free and grain free, and the cream cheese frosting is very much not optional in my house.

What makes these gluten free pumpkin cottage cheese muffins a great option for busy mornings is how effortlessly they deliver real nutrition and taste. Whipping the cottage cheese until completely smooth adds high-quality protein without changing the classic fall pumpkin bread flavor you love (especially with the cream cheese frosting). Balanced with almond flour, cassava flour, and a touch of warm cinnamon, they stay moist for days without drying out. These muffins are also freezer-friendly

If you love simple, protein-packed bakes, you will want to save a few more kitchen favorites to your weekly rotation. Try these Easy Overnight High Protein French Toast Casserole or these Gluten Free Blueberry Oatmeal Protein Pancakes  for more meal-prep, quick morning meals. Or if you are in the pumpkin or fall baking spirit, bake a loaf of my Easy Gluten Free Protein Pumpkin Bread, these Gooey Pumpkin Spice Cottage Cheese Protein Blondies, or my Dairy Free Protein Pumpkin Pie Ice Cream Ninja Creami to use up extra pumpkin puree you have leftover from these pumpkin muffins. For more cottage cheese meal-prep options, these cottage cheese recipes would be a great place to look!

Please note this post contains affiliate links.

Why You’ll Love This Pumpkin Muffin Recipe

• It's packed with protein. Made with whipped cottage cheese, eggs, almond flour, and protein powder, this pumpkin muffin recipe is a great option for anyone trying to increase their protein intake without giving up a fall sweet treat.
• It is a perfect dessert, breakfast & snack. Delicious, protein-packed, and easy to bake, making these muffins the perfect breakfast and/or snack.
• Ideal for weekly meal prep. A single batch of these muffins bakes so quickly on a Sunday, providing nutritious grab-and-go options for busy mornings or when you are needing a snack. It is also freezer-friendly (minus the frosting) so it makes this muffin even better!
• Naturally gluten free & grain free. Almond flour and cassava flour offer a wholesome alternative for anyone managing gluten sensitivities or allergies.

Pumpkin Muffins Ingredients (& Substitutions)

• 100% Pure Pumpkin Puree. This gives the muffin the perfect pumpkin taste without anything added. Do not substitute for pumpkin pie filling.
• Whipped Cottage Cheese. The secret weapon for adding moisture and extra protein without drying out the crumb of the quick bread. Simply swap the cottage cheese in the banana bread batter for a thick dairy-free yogurt for a dairy-free bread result.
• Eggs.
• Vanilla. Classic add-in for baked goods and in the frosting.
• Coconut Sugar. This recipe skips refined white sugar entirely by using coconut sugar, which adds a wonderful caramel-like depth that pairs perfectly with the spices.
• Avocado Oil. A light, neutral oil that keeps the crumb perfectly moist (especially with gluten-free flours). I do not recommend using extra-virgin olive oil as it will add a strong flavor to the cake that you don't want.
• Almond Flour & Cassava Flour. The almond flour provides moisture, while the cassava gives it that classic cake structure you know and love.
• Vanilla or Cinnamon Rolls Protein Powder. Adds sweetness and a major protein boost. Cinnamon roll protein powder would work beautifully here to boost that pumpkin bread flavor, too! My favorite brand of protein powder to use is Equip Foods. Use the code PRETTYDELISH for a discount.
• Baking Soda & Baking Powder. These are leavening agents to help the muffins rise properly.
• Salt.
• Pumpkin Spice. A perfect addition to any pumpkin bread recipe! This high protein breakfast, dessert or even a quick fall snack recipe has it all. If you don't like the combination of pumpkin spice, you can just add cinnamon for that spice flavor.
• Cream cheese. Pumpkin and cream cheese are a great flavor combination. I wouldn't recommend substituting it for anything else.
• Plain greek yogurt. You can also use skyr instead of greek yogurt. Both work amazing in this frosting.
• Maple syrup. Adds just a hint of sweetness to the frosting without adding refined sugars like powdered sugar (like normal frostings).

Pumpkin Cottage Cheese Muffin Step by Step Instructions

1. Prep. Preheat oven to 350F. Line a muffin pan with parchment paper muffin liners and set aside until the batter is ready.

2. Whip the cottage cheese. Put the cottage cheese in the food processor and blend until smooth and fluffy, about 1-2 minutes. Leave in the food processor until you are ready for it.

3. Mix the wet ingredients. Add the eggs, vanilla, whipped cottage cheese, pumpkin puree and coconut sugar to a large mixing bowl. Whisk until fully incorporated. Then whisk in the avocado oil until everything is combined.

4. Mix in the dry ingredients. Add almond flour, cassava flour, baking soda, baking powder, pumpkin spices, salt and protein powder if using to the same mixing bowl and fold together with the wet ingredients until fully combined. Make sure there are no clumps of flour or protein powder.

5. Pour Batter in Muffin Tin. Using a ¼ cup measuring cup, scoop the batter into the muffin tin until each cup is just about full. Don’t worry, since this is gluten free it won’t spill over when baking!

6. Bake. Bake for 18-20 minutes until a toothpick inserted in the center comes out clean.

7. Make the frosting. While the muffins bake, mix the frosting ingredients in a medium mixing bowl with a hand mixer on medium speed until light and fluffy.

8. Cool & Frost Muffins. Allow muffins to come to room temp before frosting to avoid melting. Frost the pumpkin muffins with your cream cheese frosting with a butter knife and enjoy!

Muffin Expert Tips & Tricks

• Don't over-mix the batter. Once the dry ingredients go into the wet ingredients, fold gently with a silicone spatula just until combined. Over-mixing leads to a tougher crumb.
• Whip the cottage cheese thoroughly. Run your food processor until no visible curds remain. A smooth consistency blends seamlessly into the wet ingredients.
• Fill the muffin cups fully: Because this batter does not spill over drastically, scoop it until each cup is almost completely filled for full-sized muffins.
• Save the leftover pumpkin puree for more pumpkin baking. Instead of wasting the last of the pumpkin puree, go ahead and save the leftover puree for a different fall treat: pumpkin loaf with cream cheese frosting, pumpkin syrup for fall coffees (bye overpriced Starbuck's drinks!), or these pumpkin blondies.
• Make a double batch and freeze half to save for later. Whenever I make my cottage cheese banana muffins or these pumpkin muffins, I always make a double batch of them and then freeze one batch for later. It makes it really easy to grab a couple at a time to thaw for a quick snack on the go or for overall meal prep when life is busy (like right now with me and my husband moving!).

Cottage Cheese Muffin Frequently Asked Questions

Are these Pumpkin Cottage Cheese Muffins gluten-free?

Yes, this pumpkin muffin recipe relies on a combination of almond flour and cassava flour, making it completely grain-free and naturally gluten-free. So if you cannot have gluten but still want a tasty to-go snack or easy breakfast, these muffins are a great option.

Do I need a food processor to blend the cottage cheese?

A food processor, high-speed blender, or immersion blender will all work effectively to remove the curds and whip the cottage cheese smooth.

Why did my gluten free muffins not rise high over the top of the tin?

Gluten-free flours like almond and cassava are denser than traditional wheat flour, so they expand less while baking. Filling each muffin tin almost full ensures a nice, rounded muffin top.

Can I make this recipe without the protein powder?

The protein powder is completely optional, but it does add more protein without changing the texture of the muffin too much. If you skip it, the batter remains well-balanced and bakes up wonderfully.

Can I use a different sweetener instead of coconut sugar?

If you want to keep this easy pumpkin muffin recipe entirely free from added refined sugars, you can swap the coconut sugar for an equal amount of granulated monkfruit. It bakes similarly and still gives you great results without the blood sugar spike. I wouldn't recommend liquid sweeteners like maple syrup, as it will change the ratio of wet to dry ingredients in the batter.

Can I add chocolate chips to this muffin instead of adding frosting?

Yes! Though the frosting is amazing with these muffins, if you are not a frosting kind of person, then yes, add those chocolate chips to the batter before baking to give it a bit of more sweetness.

How to Store These Pumpkin Muffins

Store these muffins in an airtight container or ziplock bag with air removed, in the refrigerator for about 3-5 days. Because of the cottage cheese and the cream cheese frosting, I recommend keeping them refrigerated rather than leaving them out at room temperature after the first day.

To freeze let the muffins cool completely, then wrap the individual cooled muffins without the frosting in plastic wrap or store them together in a freezer-safe bag for up to 3 months. Thaw the muffins at room temperature or warm briefly in the microwave for 30 to 60 seconds.

If you liked this cottage cheese dessert recipe, you might also enjoy:

• Easy Gluten Free Protein Pumpkin Bread 
• Gooey Pumpkin Spice Cottage Cheese Protein Blondies
• Protein Cottage Cheese Banana Muffins (Grain Free & Gluten Free)
• Protein Banana Nut Bread with Protein Cream Cheese Frosting (Easy & Gluten Free)
• Gooey Cottage Cheese Blondies Easy Protein Dessert
• High Protein Cottage Cheese Cosmic Brownies Recipe
• Or really any of these other 20+ Easy to Make High Protein Cottage Cheese Recipes

Did you have a chance to make this recipe? If so, please leave me a 5 star rating and review below. I always love and appreciate hearing from you!