Name: Cottage Cheese Pumpkin Muffins (Soft, Spiced, and with Protein)
Prep time: 10 min
Cook time: 18 min
Ingredients: 1 Cup All-Purpose Flour; 3/4 Cup Wheat Flour; 1 1/2 tsp. Cinnamon; 1/4 tsp. Nutmeg; 1/2 tsp. Allspice; 1/2 tsp. Ginger (ground); 1/4 tsp. Cloves; 1/2 tsp. Baking soda; 1 tsp. Baking powder; 1/2 tsp. Salt; 1 tsp vanilla extract; 1/2 Cup maple Syrup (or honey); 1 Cup of pumpkin purée; 1 Cup Cottage cheese; 1/2 Cup Oil (such as avocado oil); 2 eggs

Cottage cheese pumpkin muffins might sound unexpected, but the cottage cheese is what makes these so much better than your average pumpkin muffin. It blends smooth, adds protein, and keeps every single bite incredibly moist. These muffins are packed with warm spices flavor, have a tender crumb, and include added protein to start the day out right.

All the wet ingredients go into the blender for, which makes this recipe way easier than it looks. The cottage cheese blends up completely smooth, so you get that rich, moist texture in every bite without any extra work. I started making these on Sunday afternoons to stock the week, and my family goes through them fast. If you’re into make-ahead muffin recipes, my brown butter honey peach muffins are another batch-baking favorite worth trying.

Two cottage cheese pumpkin muffins stacked on each other.

Why You’ll Love This Recipe

Protein-packed: The cottage cheese blends right into the batter and adds protein you can actually feel, without changing the flavor at all.

Warm fall flavor: Cinnamon, nutmeg, allspice, ginger, and cloves give these muffins that classic cozy pumpkin spice flavor in every single bite.

Easy to make: One blender, one bowl, and about 15 minutes of prep. These healthy pumpkin muffins come together fast and bake up beautifully.

Make-ahead friendly: Bake a full batch and you have breakfast or snacks covered for a few days.

What I Love:

What I Love: These muffins use both all-purpose and wheat flour, which gives them just a little more substance and a slightly hearty texture without being heavy. It’s a small swap that makes a real difference. The muffins are also lightly sweetened with maple syrup.

The ingredients needed to make the cottage cheese pumpkin muffins.

Ingredient Notes and Substitutions

All-Purpose Flour and Wheat Flour: Using a blend of both flours gives these muffins structure while adding a little more nutrition from the wheat flour. If you need these to be gluten-free, swap both for a 1:1 gluten-free flour blend.

Pumpkin Puree: Use canned pumpkin puree, not pumpkin pie filling. Pumpkin pie filling has added sugar and spices already mixed in, which will throw off the flavor balance of the muffins.

Cottage Cheese: This is the star ingredient in these protein pumpkin muffins. It blends up completely smooth and you cannot taste it at all. Use any fat percentage you have on hand. Full-fat will give you the richest, most moist result, but 2% works great too.

Honey or Maple Syrup: Either one works here and both add a natural sweetness that pairs really well with the pumpkin spice blend.

Oil: A neutral oil is the best choice here. Avocado oil, canola oil, vegetable oil, or sunflower oil all work well. The oil keeps the muffins moist and tender.

Eggs: Two eggs provide structure and help bind everything together. I have not tested this recipe with an egg substitute.

Spices: The recipe uses a blend of spices, but you could use pumpkin spice instead. You will need about 2 teaspoons of pumpkin spice.

The blended cottage cheese and pumpkin puree next to the dry ingredients for the pumpkin muffins.

Cottage cheese pumpkin muffin batter in muffin tins before being baked.

How to Make Cottage Cheese Pumpkin Muffins: Step-by-Step Instructions

Preheat the oven to 425 degrees F. Line a 12-cup muffin tin with muffin liners.
In a large mixing bowl, combine the all-purpose flour, wheat flour, cinnamon, nutmeg, allspice, ginger, cloves, baking soda, baking powder, and salt. Whisk together until fully combined and set aside.
Add all the wet ingredients to a blender or food processor – the pumpkin puree, cottage cheese, eggs, oil, honey or maple syrup, and vanilla extract. Blend until completely smooth.
Pour the wet mixture into the dry ingredients. Stir until just combined. Be careful not to overmix.
Let the batter rest for 10 minutes. This step helps hydrate the flour and gives you taller, better-textured muffins.
Divide the batter evenly among the 12 muffin tins.
Bake at 425 degrees F for 5 minutes, then reduce the heat to 350 degrees F and bake for an additional 12-15 minutes, or until a toothpick inserted in the center comes out clean.
Remove from the oven and let cool before enjoying.

Sara’s Tip

Do not skip the batter rest! Letting the batter sit for 10 minutes before baking allows the flour to fully absorb the wet ingredients. This creates a thicker batter and gives you those tall, domed bakery-style muffin tops. If you are short on time you can skip it, but the resting step is worth it for the best results.

Up close of cottage cheese pumpkin muffin in muffin tin.

Recipe FAQs

Can I taste the cottage cheese in these muffins?

Not at all. The cottage cheese blends completely smooth and disappears right into the batter. What it leaves behind is just moisture and protein – no flavor, no texture. These muffins with cottage cheese taste just like a classic spiced pumpkin muffin.

Do I need a blender?

A blender or food processor is the easiest way to get the cottage cheese completely smooth before mixing it into the dry ingredients. If you don’t have one, you can use an immersion blender, though the texture may be slightly less smooth.

Can I use only all-purpose flour?

Yes! If you don’t have wheat flour on hand, you can use all all-purpose flour. The muffins will be a little lighter in texture. A full swap to all wheat flour will work too, but the muffins will be a bit denser.

Can I add mix-ins?

Definitely. Chocolate chips are a great addition and pair really well with the warm spice blend and will add a touch more sweetness to the muffins. Chopped walnuts or pecans would also work well. Fold them in right after combining the wet and dry ingredients. These cottage cheese protein muffins are very versatile.

Can I make these into mini muffins?

Yes! Fill a mini muffin tin about three-quarters of the way full and reduce the bake time. Start checking around 10-12 minutes total.

How do I store these?

Store the muffins in an airtight container at room temperature for up to 3 days, or in the fridge for up to 5 days. Because of the added moisture from the pumpkin and cottage cheese, I usually store mine in the fridge and just pop one in the microwave for about 15-20 seconds before eating.

Can I freeze them?

Yes! Let the muffins cool completely, then wrap each one in plastic wrap and place them in a zip lock freezer bag. They freeze well for up to 3 months. Thaw overnight in the fridge or reheat from frozen in the microwave.

If you are looking for more easy muffin recipes to add to your rotation, there are plenty to choose from on the blog.

If you give these cottage cheese pumpkin muffins a try, let me know your thoughts in the comments below!

And be sure to tag me on Instagram so I can see your creations.

From my kitchen to yours, happy baking! I hope you love these muffins for breakfast as much as we do!