Get ready to fall in love with your new favorite autumn snack! These incredible Pumpkin Protein Muffins are the perfect blend of cozy fall flavor and muscle-building power. They are incredibly moist, perfectly spiced, and packed with enough protein to keep you full and energized, whether you’re starting your day or need a post-workout refuel. Forget dry, tasteless protein snacks; this recipe delivers a tender, bakery-quality muffin you’ll make again and again.
We’ve crafted this recipe to be simple, using pantry staples you likely already have. In just over 30 minutes, you can have a batch of these healthy, delicious muffins ready to go. They are perfect for meal prep, busy mornings, or a healthy dessert. Let’s get baking!
Why You’ll Love This Pumpkin Protein Muffin Recipe
If you need more convincing, here’s why this will become your go-to recipe for healthy fall baking. These aren’t just any muffins; they are a powerhouse of flavor and nutrition.
- High in Protein: Each muffin is loaded with protein, making it an excellent choice for a satisfying breakfast or a snack to aid muscle recovery.
- Incredibly Moist: We use pumpkin puree and a touch of oil to ensure these muffins are never dry. They have a tender crumb that melts in your mouth.
- Perfectly Spiced: A warm blend of cinnamon, nutmeg, and ginger gives these muffins that classic pumpkin spice flavor everyone craves.
- Easy to Make: This is a one-bowl recipe! Simply mix the wet ingredients, then the dry, and bake. It’s practically foolproof.
- Great for Meal Prep: Bake a batch on Sunday and enjoy a healthy, grab-and-go snack all week long. For another great meal prep idea, check out this High-Protein Honey Garlic Chicken.

Ingredients You’ll Need
The magic of these Pumpkin Protein Muffins comes from a simple list of wholesome ingredients. Here’s what you’ll need to gather.
For the Wet Ingredients:
- Pumpkin Puree: The star of the show! Make sure you use 100% pure pumpkin puree, not pumpkin pie filling.
- Eggs: These bind the muffins together and provide structure.
- Maple Syrup: For natural sweetness. You can also use honey or a sugar-free syrup.
- Coconut Oil: A little bit of melted coconut oil adds necessary fat for a moist texture. Avocado oil or even melted butter works too.
- Vanilla Extract: A splash of pure vanilla extract enhances all the other flavors.
For the Dry Ingredients:
- Oat Flour: We love using oat flour for its hearty texture and nutritional benefits. You can easily make your own by blending rolled oats until fine. All-purpose or whole wheat flour also works.
- Protein Powder: Vanilla or unflavored whey or a plant-based protein powder works best. The type you use can affect the texture slightly.
- Pumpkin Pie Spice: This blend of cinnamon, nutmeg, ginger, and cloves is essential for that signature fall flavor.
- Baking Soda & Baking Powder: These leaveners help the muffins rise and become fluffy.
- Salt: A pinch of salt balances the sweetness and enhances the flavors.
How to Make Pumpkin Protein Muffins Step-by-Step
Making these muffins is as simple as mix, pour, and bake. Follow these steps for perfect results 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 non-stick spray.
- Combine Wet Ingredients: In a large mixing bowl, whisk together the pumpkin puree, eggs, maple syrup, melted coconut oil, and vanilla extract until smooth and well combined.
- Add Dry Ingredients: Add the oat flour, protein powder, pumpkin pie spice, baking soda, baking powder, and salt to the wet ingredients. Stir 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. For an extra touch, you can sprinkle some pumpkin seeds or a cinnamon-sugar mixture on top.
- Bake to Perfection: Bake for 20-25 minutes, or until a toothpick inserted into the center of a muffin comes out clean. The tops should be golden and spring back when lightly touched.
- Cool and Enjoy: Let the muffins cool in the tin for about 5 minutes before transferring them to a wire rack to cool completely.

Expert Tips for the Best Muffins
Want to elevate your pumpkin protein muffins? Here are a few tips from our kitchen to yours.
- Don’t Overmix: Overmixing the batter can develop the gluten in the flour, resulting in tough, dense muffins. Mix only until the ingredients are just combined.
- Choose the Right Protein Powder: A high-quality protein powder you enjoy the taste of is key. Whey protein tends to bake well and creates a tender texture. Plant-based powders can be more absorbent, so you may need to add an extra tablespoon of milk if the batter seems too thick.
- Measure Flour Correctly: If not using a scale, use the “spoon and level” method. Spoon the flour into your measuring cup and level it off with a knife. This prevents packing the flour, which can make muffins dry.
Variations and Customizations
This recipe is a fantastic base for your creativity. Here are some delicious ways to customize your muffins:
- Add Chocolate Chips: Fold in a half-cup of semi-sweet or dark chocolate chips for a decadent treat.
- Go Nuts: Add chopped walnuts or pecans for a delightful crunch and extra healthy fats.
- Make it Gluten-Free: Ensure you use certified gluten-free oat flour and a gluten-free protein powder.
- Sweet Toppings: A simple cream cheese frosting or a drizzle of maple glaze can turn these into a more dessert-like treat, similar to our popular Sheet Pan Pumpkin Bars.
If you’re a fan of fall baking, you might also love this Moist Pumpkin Bread Recipe.
How to Store Your Muffins
Proper storage is key to keeping your muffins fresh and delicious.
- At Room Temperature: Store the muffins in an airtight container at room temperature for up to 3 days. Placing a paper towel in the container can help absorb excess moisture.
- In the Refrigerator: For longer storage, you can refrigerate them in an airtight container for up to a week.
- For Freezing: These muffins freeze beautifully! Once completely cooled, wrap each muffin individually in plastic wrap, then place them in a freezer-safe bag or container. They will keep for up to 3 months. To enjoy, simply thaw at room temperature or microwave for 20-30 seconds.
Frequently Asked Questions
Absolutely! This recipe is naturally gluten-free as long as you use certified gluten-free oat flour. Most protein powders are gluten-free, but always check the label to be sure.
Yes, you can substitute the maple syrup with an equal amount of honey or a liquid sugar-free sweetener like monk fruit syrup. Note that this may slightly alter the flavor and texture.
Each muffin contains approximately 10 grams of protein, depending on the specific protein powder you use. This makes them a fantastic and filling snack or breakfast option.
Store your muffins in an airtight container at room temperature for up to 3 days, or in the refrigerator for up to a week. They also freeze very well for up to 3 months.
We recommend a high-quality vanilla whey protein powder as it tends to bake well and creates a moist, tender crumb. However, a plant-based vanilla protein powder will also work, though you may need to add a tablespoon of milk if the batter is too thick.
Enjoy Your Healthy Pumpkin Treat!
There you have it—a simple, healthy, and incredibly delicious recipe for Pumpkin Protein Muffins. We hope you love them as much as we do. They are the perfect way to embrace the flavors of fall while staying on track with your health goals. If you try this recipe, we’d love to hear from you! Leave a comment below or share a picture of your beautiful muffins on Pinterest. Happy baking!
Pumpkin Protein Muffins Recipe

Pumpkin Protein Muffins (Easy & Moist Recipe)
Ingredients
Equipment
Instructions
- Preheat your oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners.
- In a large mixing bowl, whisk together the pumpkin puree, eggs, maple syrup, melted coconut oil, and vanilla extract until smooth.
- Add the oat flour, protein powder, pumpkin pie spice, baking powder, baking soda, and salt to the wet ingredients. Stir 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.
Notes
Protein Powder: Whey protein typically yields the best texture. If using a plant-based powder, you may need to add a splash of milk as it can be more absorbent.
Variations: Feel free to add 1/2 cup of chocolate chips or chopped nuts to the batter.
