High Protein Pumpkin Cottage Cheese Muffins Recipe
If you’re on the lookout for a deliciously nourishing treat that powers you through the day, these High Protein Pumpkin Cottage Cheese Muffins are an absolute game changer. They blend the creamy richness of cottage cheese with the cozy, vibrant flavor of pumpkin, all while packing a serious protein punch thanks to protein powder and sprouted oats. Whether you want a hearty breakfast, a post-workout snack, or just a wholesome muffin to brighten your day, this recipe delivers moist, tender muffins with just the right sweetness and a hint of warm spices. Get ready to fall in love with every bite!

Ingredients You’ll Need
The beauty of these muffins lies in their simplicity—the ingredients are straightforward but each plays a vital role in creating the perfect balance of flavor, texture, and nutrition. From the wholesome sprouted oats that add fiber and body to the luscious organic pumpkin puree that brings moisture and color, every component counts.
- 1 ¼ cup sprouted gluten-free oats or protein oats: Provides a hearty base and boosts the protein content while keeping the texture tender.
- 2 large pasture-raised eggs: Adds structure and richness to hold the muffins together and keep them fluffy.
- 1 cup organic pumpkin puree: Brings moisture, a velvety texture, and that unmistakable autumnal flavor.
- ¾ cup full-fat, organic cottage cheese: Surprises with creamy moisture and a protein boost that keeps muffins moist and soft.
- ½ cup vanilla protein powder: Elevates protein content and adds a subtle sweetness—feel free to use code SOFRESH15 for savings!
- 1 teaspoon baking powder: Ensures the muffins rise nicely and develop a lovely light crumb.
- 1 teaspoon baking soda: Works with the acidic pumpkin puree to help the batter lift and brown evenly.
- 1 teaspoon pure vanilla extract: Adds a sweet, aromatic depth that complements the pumpkin.
- 1 teaspoon ground cinnamon: A warm, cozy spice that defines pumpkin treats.
- ½ teaspoon pumpkin spice: A blend of fragrant spices that enhances the autumn vibe.
- Optional 2-4 tablespoons coconut sugar or maple syrup: For those who love a touch of sweetness; perfect for adult palates or when serving as a dessert.
- ½ cup dark chocolate chunks + extra for topping: Adds pockets of rich, melty indulgence that contrast beautifully with the spices.
- Optional flaky sea salt for topping: A surprising sprinkle to balance sweetness and intensify flavors.
How to Make High Protein Pumpkin Cottage Cheese Muffins
Step 1: Prepare Your Oven and Muffin Pan
Start by preheating your oven to 350°F (175°C). Line a standard 12-cup muffin pan with parchment liners to ensure your muffins release easily and clean up is a breeze. A well-prepped pan makes all the difference in presentation and texture.
Step 2: Blend the Base Ingredients
Place the sprouted oats into a high-speed blender and pulse until they transform into a fine flour. This step is crucial to achieving a smooth, tender muffin crumb. Next, add the eggs, pumpkin puree, creamy cottage cheese, vanilla protein powder, baking powder, baking soda, vanilla extract, cinnamon, pumpkin spice, and maple syrup or coconut sugar if using. Blend everything together until the batter is lush, creamy, and free of oat chunks. Don’t be shy about using a spatula to scrape down the sides, making sure all ingredients are fully incorporated.
Step 3: Add the Chocolate Chunks
Remove the batter from the blender and gently fold in half a cup of dark chocolate chunks using a spatula. This adds just the right amount of decadence and surprises within each bite. The chocolate melts slightly when baked, making these muffins incredibly delightful.
Step 4: Fill the Muffin Liners and Bake
Evenly distribute the batter among the 12 parchment-lined muffin cups. For an extra indulgent look and taste, top each muffin with 2-3 chocolate chunks. Slide the pan into the oven and bake for about 20 minutes. Keep an eye on them—the muffins should turn a beautiful golden brown on top. A toothpick inserted in the center should come out clean, signaling they’re ready.
Step 5: Add the Finishing Touch
Once out of the oven, sprinkle flaky sea salt on top if desired. The salty crunch wonderfully complements the sweet and spiced flavors, making your High Protein Pumpkin Cottage Cheese Muffins unforgettable.
How to Serve High Protein Pumpkin Cottage Cheese Muffins

Garnishes
Feel free to top your muffins with an extra dusting of cinnamon or pumpkin spice for a little visual appeal and flavor boost. A drizzle of pure maple syrup can elevate them for a special breakfast treat. Freshly chopped nuts like walnuts or pecans add a delightful crunch that pairs beautifully with the soft, moist crumb.
Side Dishes
These muffins are versatile enough to accompany a variety of sides. Pair them with a dollop of Greek yogurt or cottage cheese for additional protein. Fresh fruit like apple slices or a berry medley adds refreshing brightness, while a warm cup of chai tea or coffee perfectly complements the spices.
Creative Ways to Present
For brunches or gatherings, serve the muffins on a rustic wooden board alongside small bowls of nut butters, fruit preserves, or honey. Turning them into mini muffin sandwiches with a smear of cream cheese and a slice of smoked turkey or ham makes for a unique savory-sweet option packed with protein. These muffins also travel well, making them an easy and impressive addition to picnic baskets or lunchboxes.
Make Ahead and Storage
Storing Leftovers
If you have leftover muffins, store them in an airtight container at room temperature for up to two days. Beyond that, they do best kept in the refrigerator, where they will stay fresh for up to five days. This makes them perfect for meal prep and grab-and-go snacks throughout the week.
Freezing
These High Protein Pumpkin Cottage Cheese Muffins freeze beautifully. Simply wrap each muffin individually in plastic wrap or place them in a freezer-safe zip-top bag. They can be stored in the freezer for up to three months without losing quality, making them a fantastic make-ahead option when you want to enjoy them at your convenience.
Reheating
To enjoy your muffins warm and fresh-tasting, reheat them in the microwave for 20-30 seconds or in a toaster oven at 300°F (150°C) for about 5 minutes. If frozen, allow them to thaw at room temperature for 10-15 minutes before warming. This quick reheating brings back that just-baked softness and melts any chocolate chunks to gooey perfection.
FAQs
Can I substitute the sprouted oats with regular oats?
Yes, you can use regular rolled oats, but sprouted oats have a slightly nuttier flavor and are easier to digest. If using regular oats, grinding them finely as instructed helps keep the muffins tender.
Is it necessary to add sweetener? My kids prefer less sugar.
Sweetener is optional! The natural sweetness from the pumpkin and vanilla protein powder often makes these muffins perfectly balanced. Feel free to leave out the coconut sugar or maple syrup, especially if making for kids or if you prefer a less sweet muffin.
Can I use low-fat cottage cheese instead of full-fat?
Full-fat cottage cheese adds the best moisture and richness, but low-fat can work in a pinch. Just be aware the muffins might be slightly less moist and creamy.
What protein powder works best for this recipe?
A mild vanilla-flavored whey or plant-based protein powder works great here. Choose a clean powder without an overpowering aftertaste to let the pumpkin and spices shine through.
Are these muffins gluten-free?
Yes, as long as you use gluten-free oats and protein powder, these muffins are gluten-free and suitable for those with gluten sensitivities.
Final Thoughts
These High Protein Pumpkin Cottage Cheese Muffins have quickly become one of my absolute favorite ways to enjoy pumpkin in a wholesome, protein-packed way. They’re moist, flavorful, and full of nourishing ingredients that keep you energized and satisfied. I encourage you to give this recipe a try—you might just find your new go-to breakfast or snack that will brighten your mornings and keep hunger at bay with every bite!
PrintHigh Protein Pumpkin Cottage Cheese Muffins Recipe
These High Protein Pumpkin Cottage Cheese Muffins are a delicious and nutritious treat packed with wholesome ingredients. Combining gluten-free oats, organic pumpkin puree, and protein-rich cottage cheese and protein powder, these muffins offer a moist texture and a perfect balance of sweet and spice. Ideal for breakfast, snacks, or post-workout fuel, they feature indulgent dark chocolate chunks while being naturally gluten-free and high in protein.
- Prep Time: 10 minutes
- Cook Time: 20 minutes
- Total Time: 30 minutes
- Yield: 12 muffins 1x
- Category: Breakfast, Snack
- Method: Baking
- Cuisine: American
- Diet: Gluten Free
Ingredients
Dry Ingredients
- 1 ¼ cup sprouted gluten-free oats or protein oats
- ½ cup vanilla protein powder
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- 1 teaspoon ground cinnamon
- ½ teaspoon pumpkin spice
- Optional: 2-4 tablespoons coconut sugar or maple syrup
- ½ cup dark chocolate chunks + additional for topping
- Optional flaky sea salt for topping
Wet Ingredients
- 2 large pasture-raised eggs
- 1 cup organic pumpkin puree
- ¾ cup full-fat organic cottage cheese
- 1 teaspoon pure vanilla extract
Instructions
- Preheat Oven and Prepare Pan: Preheat your oven to 350°F (175°C) and line a muffin pan with twelve parchment liners to make removal easy and prevent sticking.
- Make Oat Flour: Place the sprouted gluten-free oats into a high-speed blender and pulse until the oats turn into a fine flour-like consistency.
- Blend Wet and Dry Ingredients: Add the eggs, pumpkin puree, cottage cheese, vanilla protein powder, baking powder, baking soda, ground cinnamon, pumpkin spice, vanilla extract, and optional sweetener (coconut sugar or maple syrup) into the blender with the oat flour. Blend the mixture until it becomes creamy and smooth, using a spatula to scrape down the sides as needed to ensure everything is well combined.
- Incorporate Chocolate Chunks: Transfer the batter to a mixing bowl and gently fold in ½ cup of dark chocolate chunks using a spatula for even distribution.
- Fill Muffin Cups: Evenly divide the batter among the twelve parchment-lined muffin cups. Optionally, top each muffin with 2-3 extra chocolate chunks for added texture and chocolate flavor.
- Bake: Place the muffin pan in the preheated oven and bake for 20 minutes or until the muffin tops are golden brown and a toothpick inserted into the center comes out clean.
- Cool and Serve: Remove the muffins from the oven and allow them to cool slightly. Optionally, sprinkle with flaky sea salt before serving to enhance the flavor profile. Enjoy warm or at room temperature.
Notes
- Using sprouted gluten-free oats helps improve digestibility and nutritional value.
- Omitting the optional coconut sugar or maple syrup makes these muffins less sweet, ideal for kids or lower-sugar diets.
- Full-fat cottage cheese adds moisture and protein; do not substitute with low-fat varieties to maintain texture.
- Ensure to pulse oats finely for a smooth batter and even crumb structure.
- These muffins can be stored in an airtight container in the refrigerator for up to 5 days or frozen for up to 3 months.
- Use high-quality dark chocolate chunks with at least 70% cocoa for best taste and health benefits.
Nutrition
- Serving Size: 1 muffin
- Calories: 180
- Sugar: 5g
- Sodium: 120mg
- Fat: 7g
- Saturated Fat: 3g
- Unsaturated Fat: 4g
- Trans Fat: 0g
- Carbohydrates: 18g
- Fiber: 3g
- Protein: 12g
- Cholesterol: 70mg
Keywords: pumpkin muffins, high protein muffins, gluten free muffins, cottage cheese muffins, healthy pumpkin recipe, protein oats, fall baking