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High-Protein, Cottage Cheese Pumpkin Muffins – Healthy, Moist & Naturally Sweetened

Muffins can be indulgent, fluffy, comforting… but what if they could also be healthy, protein-packed, and nutrient-dense? Meet your new favorite fall snack: High-Protein, Cottage Cheese Pumpkin Muffins. Made with wholesome ingredients like pumpkin purée, oat flour, and low-fat cottage cheese, these muffins are moist, subtly spiced, and naturally sweetened with a touch of maple syrup. Whether you’re fueling up for the day, packing a school snack, or prepping for the week ahead, these muffins offer balanced nutrition without sacrificing flavor. They’re pork-free, alcohol-free, easy to whip up, and ideal for busy mornings, post-workout bites, or cozy fall baking days. And yes, they’re incredibly kid-friendly too!
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Prep Time 10 minutes
Cook Time 25 minutes
Cooling Time 10 minutes
Total Time 45 minutes
Servings: 12 muffins
Ingredients Equipment Method Notes

Ingredients
  

  • Here’s the complete list of ingredients to make 12 soft spiced, high-protein pumpkin muffins:
Wet Ingredients:
  • 1 cup pumpkin purée unsweetened
  • ½ cup low-fat cottage cheese
  • 2 large eggs
  • 2 tbsp maple syrup
Dry Ingredients:
  • ¾ cup oat flour
  • 1 tsp baking powder
  • 1 tsp ground cinnamon
  • ¼ tsp ground nutmeg
  • ⅛ tsp ground cloves
  • 1 pinch salt
Topping:
  • ¼ cup pumpkin seeds pepitas
  • Note: You can blend the cottage cheese for a smoother texture or leave it as is for a bit of added creaminess and chunkiness in the muffin.

Equipment

  • Here’s what you’ll need to prepare these protein-packed pumpkin muffins:
  • Medium mixing bowl
  • Whisk
  • Silicone spatula or wooden spoon
  • Measuring cups and spoons
  • Blender or food processor (optional for smoother texture)
  • Muffin tin (12-cup)
  • Muffin liners or nonstick spray
  • Oven

Method
 

  1. These muffins are as easy to make as they are delicious! Follow the steps below for moist, fluffy, and protein-rich results.
Step 1: Preheat and Prep
  1. Preheat your oven to 350°F (175°C).
  2. Line your muffin tin with paper liners or lightly grease with nonstick spray.
Step 2: Mix Wet Ingredients
  1. In a medium bowl, whisk together the pumpkin purée, cottage cheese, eggs, and maple syrup.
  2. Mix until the ingredients are well combined. You can blend the wet ingredients if you prefer a completely smooth muffin.
Step 3: Add Dry Ingredients
  1. Add the oat flour, baking powder, cinnamon, nutmeg, cloves, and salt to the wet mixture.
  2. Stir gently with a spatula until just combined. Do not overmix.
Step 4: Fill the Muffin Cups
  1. Scoop the batter evenly into the 12 muffin cups. Each should be about ¾ full.
  2. Sprinkle pumpkin seeds on top of each muffin for a crunchy, nutty finish.
Step 5: Bake
  1. Bake in the preheated oven for 20–25 minutes, or until a toothpick inserted in the center comes out clean.
  2. The tops should be firm and slightly golden.
Step 6: Cool & Serve
  1. Let the muffins cool in the tin for 5 minutes before transferring them to a wire rack.
  2. Cool completely before storing. Serve warm, room temp, or chilled—your choice!

Notes

🧊 Storage & Reheating
Storage:
Room Temperature: Store in an airtight container for up to 2 days.
Refrigerator: Keeps fresh for 5–6 days.
Freezer: Freeze in a sealed container or bag for up to 2 months. Wrap individually for easy grab-and-go.
Reheating:
Microwave: Warm a muffin for 15–20 seconds for a soft, just-baked feel.
Oven: Reheat at 300°F (150°C) for 5–7 minutes for a slightly crisp top.
🥄 Variations
Make this recipe your own with these easy, healthy twists:
Add-Ins:
Chopped walnuts or pecans for more crunch
Mini chocolate chips for a sweet touch
Chia seeds or flaxseeds for extra fiber
Dairy-Free Option:
Replace cottage cheese with dairy-free Greek-style yogurt or blended silken tofu (use same amount)
Gluten-Free Version:
Use certified gluten-free oat flour
Extra Protein:
Add 1 scoop of unflavored or vanilla plant-based protein powder and 1–2 tbsp more liquid (like almond milk) to keep it moist.
Lower Sugar:
Replace maple syrup with a mashed ripe banana for natural sweetness
❓ 10 FAQs
1. Can I taste the cottage cheese in the muffins?
No, not really. Cottage cheese blends in and gives the muffins moisture and protein without a strong flavor.
2. Can I use Greek yogurt instead of cottage cheese?
Yes! Use the same amount. The texture may be a bit smoother and more cake-like.
3. Is this recipe kid-friendly?
Absolutely! These muffins are soft, not too sweet, and packed with hidden nutrients—perfect for lunchboxes or picky eaters.
4. Can I double the recipe?
Yes. Simply double all ingredients and bake in two muffin trays. The baking time stays the same.
5. What can I use instead of oat flour?
You can use whole wheat flour or a gluten-free all-purpose flour blend. Almond flour may work, but the texture will be more delicate.
6. How much protein is in each muffin?
Approximately 6–8g of protein per muffin, depending on the brand of cottage cheese used.
7. Are these muffins freezer-friendly?
Yes. Wrap individually in plastic wrap or foil and store in a freezer-safe bag. Thaw overnight or microwave before eating.
8. Can I add a topping glaze or frosting?
Sure! A light Greek yogurt and maple drizzle would complement these muffins beautifully.
9. Can I use canned pumpkin pie filling instead of purée?
It’s not recommended. Pumpkin pie filling contains added sugar and spices, which can throw off the balance of the recipe.
10. Can I bake these in mini muffin tins?
Yes! Reduce the baking time to 12–15 minutes and check doneness with a toothpick.
🏁 Conclusion
These High-Protein, Cottage Cheese Pumpkin Muffins bring together comfort, convenience, and clean nutrition all in one bite. With a moist crumb, rich pumpkin flavor, and the added creaminess from cottage cheese, they’re a fall favorite you can feel good about.
Whether you're aiming for better breakfast choices, healthier snacks, or creative ways to use up pumpkin purée, these muffins deliver. Packed with protein and fiber, they're satisfying enough to keep you full—and tasty enough to crave every day of the week.
Bake a batch, store them up, and enjoy them any time of day—no guilt, all flavor.