High Protein Pumpkin Cottage Cheese Muffins Recipe
If you’re on the hunt for a nutrient-packed treat that somehow feels indulgent yet fuels your body, these High Protein Pumpkin Cottage Cheese Muffins might just become your new obsession. Picture tender, moist muffins bursting with the warm flavors of pumpkin and spice, enriched with creamy cottage cheese and protein powder for a satisfying boost. They effortlessly blend wholesome ingredients with a hint of sweetness and a touch of chocolate, delivering a perfect snack or breakfast that satisfies both your taste buds and your nutritional goals.

Ingredients You’ll Need
These ingredients are simple yet carefully chosen to create the perfect balance of taste, texture, and nutrition in your muffins. Each one plays a vital role in making these muffins wonderfully fluffy, flavorful, and packed with protein.
- 1 ¼ cup sprouted gluten-free oats or protein oats: Ground into flour, they provide a hearty base and subtle nuttiness.
- 2 large pasture-raised eggs: Act as the binder while adding richness and structure.
- 1 cup organic pumpkin puree: Brings that vibrant color, natural sweetness, and famous fall flavor.
- ¾ cup full-fat, organic cottage cheese: Adds moisture, creaminess, and a creamy protein punch.
- ½ cup vanilla protein powder: Boosts the protein content while keeping the muffins tender and flavorful.
- 1 teaspoon baking powder: Helps the muffins rise beautifully and stay light.
- 1 teaspoon baking soda: Balances acidity for a perfect crumb texture.
- 1 teaspoon pure vanilla extract: Enhances the sweet and warm flavor profile.
- 1 teaspoon ground cinnamon: Adds cozy spice notes that complement pumpkin perfectly.
- ½ teaspoon pumpkin spice: A classic blend to deepen the autumnal flavor.
- Optional 2-4 tablespoons coconut sugar or maple syrup: Sweetens to your preference; great if you want a hint of sweetness.
- ½ cup dark chocolate chunks + handful for topping: For a delightful, melty surprise in every bite.
- Optional flaky sea salt for topping: A sprinkle on top enhances all the flavors and balances the sweetness.
How to Make High Protein Pumpkin Cottage Cheese Muffins
Step 1: Prep and Blend
First things first, preheat your oven to 350°F and line a muffin pan with 12 parchment liners. Next, you’ll want to turn your oats into a fine flour using a high-speed blender—this creates that perfect muffin texture without needing traditional flour. To that oat flour, add the eggs, pumpkin puree, creamy cottage cheese, vanilla protein powder, baking powder, baking soda, warming spices, vanilla extract, and coconut sugar or maple syrup if you’re using it. Blend everything until the batter is luxuriously smooth and creamy, scraping down the sides as needed to get everything incorporated just right.
Step 2: Stir in the Chocolate
Once your batter is beautifully smooth, gently fold in the dark chocolate chunks with a spatula. This step is key because it ensures those gooey, rich chunks get evenly distributed throughout the muffins, gifting each bite with that perfect chocolatey surprise.
Step 3: Bake to Perfection
Evenly divide the batter among the 12 parchment-lined muffin cups. For a little extra indulgence, press 2 to 3 chocolate chunks on top of each muffin before baking. Pop the pan into your preheated oven and bake for about 20 minutes. Keep an eye on them—the muffins are done when they turn a golden brown on top, and a toothpick inserted in the center comes out clean. If you love balancing sweet and salty, sprinkle some flaky sea salt on top right after they come out of the oven.
How to Serve High Protein Pumpkin Cottage Cheese Muffins

Garnishes
Elevate your muffins with simple garnishes like a light drizzle of maple syrup or a dusting of cinnamon sugar. If you want to enjoy them cold, a smear of cream cheese or almond butter pairs wonderfully with the pumpkin and chocolate flavors, adding creaminess and richness.
Side Dishes
These muffins make a fantastic pairing with a hot cup of coffee or chai tea to complement the spice notes. You can also serve them with a side of fresh fruit, like crisp apples or juicy pears, for a balanced breakfast or snack that feels both satisfying and nourishing.
Creative Ways to Present
Turn your High Protein Pumpkin Cottage Cheese Muffins into a breakfast parfait by layering crumbled muffin pieces with Greek yogurt and a handful of granola. Another fun idea is to slice them in half and use as a base for mini pumpkin-inspired breakfast sandwiches with nut butter, banana slices, or turkey bacon.
Make Ahead and Storage
Storing Leftovers
If you happen to have any extras (which might be tough!), store your muffins in an airtight container at room temperature for up to two days. For longer freshness, keep them refrigerated where they’ll stay good for about 5 days, maintaining their moist texture and rich flavors.
Freezing
These muffins freeze beautifully, making them a fantastic make-ahead option. Simply wrap each muffin tightly in plastic wrap or place them in a freezer bag, then freeze for up to 3 months. When you’re ready for a quick snack or breakfast, just thaw overnight in the fridge or gently warm them up straight from the freezer.
Reheating
To bring back that just-baked warmth and softness, reheat your muffins in the microwave for 20-30 seconds or warm them in a 325°F oven for about 10 minutes. The chocolate chunks will get melty and the spices will smell irresistible.
FAQs
Are these muffins gluten-free?
Yes! By using sprouted gluten-free oats or a protein oat blend, these muffins are naturally gluten-free, making them a great choice for those avoiding gluten.
Can I substitute the cottage cheese?
If you don’t have cottage cheese, Greek yogurt is a reasonable substitute, though it may slightly change the texture and moisture level of the muffins.
Is the protein powder necessary?
While the protein powder boosts the nutritional profile of these muffins, you can leave it out or replace it with an equal amount of oat flour if you prefer. Just keep in mind that the protein content will be lower.
Can I make these muffins vegan?
These muffins rely on eggs and cottage cheese for their texture and protein, so converting them vegan would require significant ingredient swaps and might not yield the same fluffy richness.
How do I know when the muffins are done baking?
Look for golden brown tops and a toothpick inserted into the center to come out clean. This usually takes about 20 minutes, but keep an eye toward the end of baking times to avoid overcooking.
Final Thoughts
These High Protein Pumpkin Cottage Cheese Muffins have quickly become one of my favorite ways to enjoy pumpkin anytime of the year. They are wonderfully wholesome but feel like a treat, perfect for starting your day or fueling your afternoon. Once you try them, you’ll understand why I keep coming back for more—they are just that good and that good for you. Give them a whirl and watch how effortlessly they become a staple in your baking rotation!
PrintHigh Protein Pumpkin Cottage Cheese Muffins Recipe
These High Protein Pumpkin Cottage Cheese Muffins are a delicious and nutritious treat perfect for breakfast or a wholesome snack. Packed with protein from cottage cheese and protein powder, combined with fiber-rich oats and seasonal pumpkin puree, these muffins offer a moist texture and a subtly spiced flavor. Enhanced with dark chocolate chunks and optional coconut sugar or maple syrup, they balance health and indulgence beautifully.
- 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
Wet Ingredients
- 2 large pasture-raised eggs
- 1 cup organic pumpkin puree
- ¾ cup full-fat, organic cottage cheese
- 1 teaspoon pure vanilla extract
Optional Toppings
- Flaky sea salt for topping
Instructions
- Preheat Oven and Prepare Muffin Pan: Preheat your oven to 350°F (175°C) and line a muffin pan with 12 parchment liners to prevent sticking.
- Make Oat Flour: Add the sprouted gluten-free oats into a high-speed blender and pulse until they reach a fine, flour-like consistency.
- Blend Wet and Dry Ingredients: To the oat flour in the blender, add the eggs, pumpkin puree, cottage cheese, vanilla protein powder, baking powder, baking soda, cinnamon, pumpkin spice, vanilla extract, and coconut sugar or maple syrup if using. Blend until the batter is creamy, smooth, and well combined. Use a spatula to scrape down the sides to ensure even mixing.
- Incorporate Chocolate Chunks: Transfer the batter to a bowl and gently fold in the dark chocolate chunks with a spatula for an even distribution throughout the batter.
- Fill Muffin Liners: Evenly spoon the batter into the 12 prepared muffin liners, filling each about three-quarters full. Top each muffin with 2-3 extra chocolate chunks if desired.
- Bake the Muffins: Place the muffin pan in the oven and bake for approximately 20 minutes, or until the tops turn golden brown and a toothpick inserted into the center comes out clean.
- Cool and Serve: Remove the muffins from the oven, optionally sprinkle with flaky sea salt for a perfect sweet-salty contrast, and allow them to cool briefly before serving.
Notes
- These muffins are moist and best enjoyed within 2-3 days; store in an airtight container in the refrigerator.
- For a vegan version, substitute eggs with flax eggs and use a plant-based protein powder and dairy-free cottage cheese alternative.
- Adjust sweetness to taste; you can omit coconut sugar or maple syrup if you prefer less sweet muffins.
- Using sprouted oats increases digestibility and nutrition but regular oats can be used if unavailable.
- The addition of flaky sea salt enhances the chocolate flavor and balances sweetness.
Nutrition
- Serving Size: 1 muffin
- Calories: 180 kcal
- Sugar: 4 g
- Sodium: 120 mg
- Fat: 7 g
- Saturated Fat: 3 g
- Unsaturated Fat: 3 g
- Trans Fat: 0 g
- Carbohydrates: 18 g
- Fiber: 3 g
- Protein: 12 g
- Cholesterol: 55 mg
Keywords: high protein muffins, pumpkin muffins, cottage cheese muffins, gluten-free breakfast, healthy pumpkin recipe, protein-packed snacks