Get ready to transform your breakfast routine with these incredible pumpkin protein muffins. They are perfectly moist, packed with warm spices, and loaded with protein to keep you full and energized all morning. This recipe is simple to follow and guarantees a delicious, healthy treat the whole family will love. Forget dry, bland protein snacks; these muffins are a game-changer.
We’re using simple, wholesome ingredients to create a batch of fluffy, flavorful muffins that are perfect for meal prep. Whether you need a quick grab-and-go breakfast or a satisfying post-workout snack, this recipe is the answer. Plus, your kitchen will smell absolutely amazing!

Why This Is the Best Pumpkin Protein Muffins Recipe
You’re going to fall in love with this recipe, and here’s why. We’ve tested and perfected this formula to ensure it’s not just healthy but also incredibly delicious.
- High in Protein: Each muffin is packed with protein, helping you meet your fitness goals while enjoying a tasty treat.
- Incredibly Moist: Thanks to the pumpkin puree and Greek yogurt, these muffins have a tender, moist crumb that stays fresh for days.
- Easy to Make: This is a one-bowl recipe that comes together in minutes. No complicated steps, just mix, pour, and bake!
- Perfect for Meal Prep: Make a batch on Sunday and enjoy a healthy, pre-portioned breakfast or snack all week long. They are a fantastic alternative to our popular fluffy blueberry muffins when you’re craving fall flavors.
Key Ingredients You’ll Need
This recipe uses pantry staples to create wonderfully spiced and delicious pumpkin protein muffins. Here’s a breakdown of what you’ll need.
For the Wet Ingredients
- Pumpkin Puree: The star of the show! Use 100% pure pumpkin puree, not pumpkin pie filling, for authentic flavor and moisture.
- Greek Yogurt: This adds extra protein and makes the muffins incredibly moist. Use plain, unsweetened Greek yogurt.
- Eggs: They bind everything together and help the muffins rise.
- Maple Syrup: A natural sweetener that pairs perfectly with pumpkin and spice.
- Coconut Oil: Provides healthy fats and a tender texture. You can also use melted butter.
- Vanilla Extract: A splash of vanilla enhances all the other flavors.
For the Dry Ingredients
- Protein Powder: Vanilla or unflavored whey or a plant-based protein powder works best. The type you use can affect the texture slightly, so choose one you enjoy.
- Whole Wheat Flour: Adds fiber and a slightly nutty flavor. You can also use all-purpose flour or a 1:1 gluten-free baking flour.
- Pumpkin Pie Spice: This classic blend of cinnamon, nutmeg, ginger, and cloves gives the muffins their signature warm flavor.
- Baking Soda & Baking Powder: The leavening agents that make the muffins light and fluffy.
- Salt: A pinch of salt balances the sweetness and enhances the overall flavor.

Step-by-Step Instructions to Make Pumpkin Protein Muffins
Making these healthy pumpkin protein muffins is incredibly straightforward. Just follow these simple steps for a perfect batch every time.
- Preheat and Prep: First, preheat your oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease it well with cooking spray.
- Combine Wet Ingredients: In a large mixing bowl, whisk together the pumpkin puree, Greek yogurt, eggs, maple syrup, melted coconut oil, and vanilla extract until smooth and well combined.
- Combine Dry Ingredients: In a separate bowl, stir together the whole wheat flour, protein powder, pumpkin pie spice, baking soda, baking powder, and salt.
- Mix Wet and Dry: Add the dry ingredients to the wet ingredients. Mix gently with a spatula until just combined. Be careful not to overmix; a few lumps are perfectly fine.
- Fill Muffin Tin: Evenly divide the batter among the 12 prepared muffin cups. They should be about two-thirds full.
- Bake to Perfection: Bake for 20-25 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
- Cool and Enjoy: Let the muffins cool in the tin for a few minutes before transferring them to a wire rack to cool completely.
Expert Tips for Perfect Muffins
- Don’t Overmix the Batter: Overmixing develops the gluten in the flour, which can lead to tough, dense muffins. Mix only until the flour is no longer visible.
- Measure Flour Correctly: For the best results, spoon the flour into your measuring cup and level it off with a knife. This prevents packing the flour, which can make the muffins dry.
- Protein Powder Matters: Different protein powders absorb liquid differently. If your batter seems too thick, add a tablespoon or two of milk (dairy or non-dairy) until it reaches a thick but scoopable consistency.
- Add Some Toppings: Before baking, feel free to sprinkle the tops with a few chocolate chips, chopped nuts, or pumpkin seeds for extra texture and flavor. For a different but equally delicious breakfast, consider trying this amazing cinnamon apple bread.
How to Store & Freeze Your Muffins
One of the best things about these pumpkin protein muffins is how well they store. To keep them fresh, place them in an airtight container at room temperature for up to 3 days. For longer storage, you can refrigerate them for up to a week.
These muffins are also freezer-friendly! To freeze, wrap each muffin individually in plastic wrap and then place them in a freezer-safe bag. They will keep for up to 3 months. To enjoy, simply thaw at room temperature or warm in the microwave for 20-30 seconds. This makes them a perfect component for your healthy weekly meal prep.
Frequently Asked Questions
We recommend using a vanilla or unflavored whey, casein, or a plant-based blend you enjoy the taste of. Different protein powders can absorb liquid differently, so you may need to add a splash of milk if your batter seems too thick.
Yes, absolutely! To make these muffins gluten-free, simply substitute the whole wheat flour with a high-quality 1-to-1 gluten-free baking flour. The results will be just as delicious.
You can, but you’ll need to cook and puree it first. Ensure the final puree is thick and not watery, similar to the consistency of canned pumpkin puree, as excess water can make the muffins too dense.
This recipe is already refined-sugar-free as it uses pure maple syrup as the primary sweetener. You could also use honey or a sugar-free maple syrup alternative if you prefer.
These muffins are very versatile! Some great mix-ins include chocolate chips, chopped pecans or walnuts, dried cranberries, or a handful of pumpkin seeds for a crunchy topping.
More Recipes You’ll Love
We hope you loved this easy recipe for pumpkin protein muffins! If you did, leave a comment below and let us know what you think. We’d love for you to share it on Pinterest too!

Pumpkin Protein Muffins Recipe

Pumpkin Protein Muffins (Easy & Healthy Recipe)
Ingredients
Equipment
Method
- Preheat your oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease it with cooking spray.
- In a large mixing bowl, whisk together the pumpkin puree, Greek yogurt, eggs, maple syrup, melted coconut oil, and vanilla extract until smooth.
- In a separate bowl, stir together the whole wheat flour, protein powder, pumpkin pie spice, baking soda, baking powder, and salt.
- Add the dry ingredients to the wet ingredients and mix with a spatula until just combined. Do not overmix.
- Divide the batter evenly among the 12 muffin cups.
- Bake for 20-25 minutes, or until a toothpick inserted into the center comes out clean.
- Let the muffins cool in the tin for 5 minutes before transferring them to a wire rack to cool completely.
Nutrition
Notes
Protein Powder Choice: The type of protein powder can alter the texture. Add a splash of milk if the batter is too thick.
Storage: Store in an airtight container at room temperature for up to 3 days or freeze for up to 3 months.












