Pumpkin Protein Muffins (The Ultimate Healthy Recipe)

By Natalie Quinn

On December 24, 2025

A close-up shot of a fluffy pumpkin protein muffin studded with chocolate chips, sitting next to a glass of milk on a rustic wooden table.

Cuisine

American

Prep time

10 minutes

Cooking time

22 minutes

Total time

32 minutes

Servings

12 muffins

Get ready to fall in love with your new favorite grab-and-go breakfast. These incredible Pumpkin Protein Muffins are the perfect blend of cozy autumn flavor and muscle-building power. They’re unbelievably moist, packed with warm spices, and so easy to whip up for a healthy start to your day or a satisfying afternoon snack. Forget dry, bland protein treats; this recipe delivers a tender, flavorful muffin you’ll actually crave.

We’ve crafted this recipe to be simple, satisfying, and perfect for meal prep. In just over 30 minutes, you can have a batch of these delicious muffins ready for the week. They’re a fantastic way to use up leftover pumpkin puree and get a serious protein boost without sacrificing flavor.

Why You’ll Love These Pumpkin Protein Muffins

If you’re looking for a healthy recipe that doesn’t taste “healthy,” this is it. These muffins are a game-changer for busy mornings and fitness enthusiasts alike.

  • High in Protein: Each muffin is loaded with protein to keep you full, focused, and energized for hours. It’s the perfect way to fuel your post-workout recovery or power through a midday slump.
  • Incredibly Moist & Fluffy: Thanks to the pumpkin puree and a perfect balance of ingredients, these muffins have a tender, bakery-quality crumb that’s never dry.
  • Easy to Make: This is a one-bowl recipe! Simply mix the wet ingredients, fold in the dry, and bake. No complicated steps required.
  • Perfect for Meal Prep: Bake a batch on Sunday and enjoy a healthy, pre-portioned breakfast or snack all week long. They store and freeze beautifully. Looking for another great breakfast meal prep idea? Try these amazing Sausage, Egg, and Cheese Roll-Ups.
The batter for pumpkin protein muffins being mixed in a large bowl, showing the pumpkin puree, flour, and spices before being combined.
This one-bowl recipe is incredibly easy to whip up.

Key Ingredients You’ll Need

This recipe uses simple, wholesome ingredients you might already have in your pantry, especially during the fall season.

For the Muffins:

  • Pumpkin Puree: The star of the show! Use 100% pure pumpkin puree, not pumpkin pie filling, for that authentic flavor and moisture.
  • Protein Powder: Vanilla or unflavored whey protein powder works best to complement the pumpkin and spices without being overpowering.
  • Flour: All-purpose flour provides the structure. You can also experiment with whole wheat or a gluten-free blend.
  • Eggs: They bind the ingredients together and add richness.
  • Maple Syrup: A natural sweetener that pairs perfectly with pumpkin.
  • Coconut Oil: Adds healthy fats and ensures a moist texture.
  • Pumpkin Pie Spice: A classic blend of cinnamon, nutmeg, ginger, and cloves that screams autumn. If you love pumpkin spice, you must try this Super Moist Pumpkin Bread Recipe.
  • Baking Soda & Baking Powder: The leavening agents that make the muffins rise and become fluffy.
  • Salt: A pinch to enhance all the other flavors.

Optional Add-ins:

  • Chocolate Chips: Dark or semi-sweet chocolate chips make these muffins extra decadent.
  • Nuts: Chopped pecans or walnuts add a delightful crunch.
  • Seeds: A sprinkle of pumpkin seeds (pepitas) on top before baking looks beautiful and adds texture.

Choosing the Right Protein Powder

The type of protein powder you use can affect the texture of your Pumpkin Protein Muffins. Whey protein tends to yield a fluffier, more tender result as it absorbs less moisture than casein or some plant-based proteins. If using a plant-based powder (like pea or brown rice protein), you may need to add an extra splash of milk or a tablespoon of pumpkin puree to ensure the batter isn’t too thick. Always choose a powder with a flavor you enjoy on its own!

A close-up shot of a fluffy pumpkin protein muffin studded with chocolate chips, sitting next to a glass of milk on a rustic wooden table.
Look at that perfectly moist and fluffy texture!

How to Make Pumpkin Protein Muffins (Step-by-Step)

Making these muffins couldn’t be simpler. Just follow these easy steps for perfect results every time.

  1. 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.
  2. Mix Wet Ingredients: In a large mixing bowl, whisk together the pumpkin puree, eggs, melted coconut oil, and maple syrup until smooth and well combined.
  3. Combine Dry Ingredients: Add the all-purpose flour, protein powder, pumpkin pie spice, baking soda, baking powder, and salt to the same bowl.
  4. Fold to Combine: Gently fold the dry ingredients into the wet ingredients with a spatula until just combined. Be careful not to overmix; a few small lumps are okay. If you’re using any add-ins like chocolate chips or nuts, fold them in now.
  5. Fill Muffin Tin: Divide the batter evenly among the 12 prepared muffin cups, filling each about three-quarters full.
  6. Bake: Transfer the muffin tin to the preheated oven and bake for 18-22 minutes. You’ll know they’re done when a toothpick inserted into the center of a muffin comes out clean.
  7. Cool: Let the muffins cool in the tin for about 5 minutes before transferring them to a wire rack to cool completely.

Tips for Perfectly Moist Muffins

Keep these simple tips in mind to ensure your protein muffins are the best they can be.

  • Don’t Overmix the Batter: Overmixing develops 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. Scooping directly from the bag can pack the flour and make your muffins dry.
  • Check for Doneness: Ovens can vary. Start checking your muffins at the 18-minute mark to avoid overbaking.

Ingredient Substitutions & Variations

This recipe is incredibly versatile. Feel free to customize it to your liking or dietary needs.

  • Gluten-Free: Swap the all-purpose flour with a 1-to-1 gluten-free baking flour blend.
  • Dairy-Free: Ensure you use a dairy-free protein powder and coconut oil (as listed).
  • Sweeteners: You can substitute maple syrup with honey or agave nectar. For a lower-sugar option, use a monk fruit-based liquid sweetener.
  • Spices: If you don’t have pumpkin pie spice, use 1 ½ teaspoons of cinnamon plus ½ teaspoon each of nutmeg and ginger.

For another easy and delicious muffin recipe, check out our Easiest Blueberry Muffins. They are always a crowd-pleaser!

Storage and Freezing Instructions

These muffins are perfect for making ahead. To store, let them cool completely and 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.

To freeze, wrap each cooled muffin individually in plastic wrap, then place them in a freezer-safe bag or container. They will keep in the freezer for up to 3 months. To enjoy, simply thaw at room temperature or warm in the microwave for 20-30 seconds.

Frequently Asked Questions

Yes, these muffins are a great healthy option. They are high in protein, which helps with satiety, and use natural sweeteners like maple syrup and pumpkin puree for flavor and moisture, making them a balanced choice for breakfast or a snack.

Yes, you can omit the protein powder. If you do, replace the 1/2 cup of protein powder with an additional 1/2 cup of all-purpose flour to maintain the batter’s consistency.

Absolutely! You can easily make this recipe gluten-free by substituting the all-purpose flour with a 1-to-1 gluten-free baking flour blend. The results will be just as delicious.

Store the cooled 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 using a vanilla or unflavored whey protein powder for the best texture and flavor. Whey protein tends to create a lighter, fluffier muffin. If you use a plant-based protein, you might need to add a little extra liquid as they can be more absorbent.

More Delicious & Healthy Recipes to Try

If you enjoyed these muffins, you’ll love these other simple and flavorful recipes:

Enjoy Your Homemade Pumpkin Protein Muffins!

This recipe is more than just a snack; it’s a delicious way to nourish your body and embrace the cozy flavors of the season. We hope you love these Pumpkin Protein Muffins as much as we do. If you try them, please leave a comment below and let us know what you think! For more recipe inspiration, be sure to follow us on Pinterest.

A stack of delicious pumpkin protein muffins on a plate, with one muffin cut open to show its moist and fluffy texture. Perfect for a healthy fall breakfast or snack.
The best pumpkin protein muffins for a healthy and satisfying treat!

Pumpkin Protein Muffins Recipe

A close-up shot of a fluffy pumpkin protein muffin studded with chocolate chips, sitting next to a glass of milk on a rustic wooden table.

Pumpkin Protein Muffins (The Ultimate Healthy Recipe)

These unbelievably moist and fluffy Pumpkin Protein Muffins are packed with warm spices and a serious protein boost. The perfect easy recipe for a healthy breakfast or snack.
Prep Time 10 minutes
Cook Time 22 minutes
Total Time 32 minutes
Servings: 12 muffins
Course: Breakfast, Snack
Cuisine: American
Calories: 155

Ingredients
  

  • 1 cup pumpkin puree not pumpkin pie filling
  • 2 large eggs
  • 1/2 cup maple syrup
  • 1/4 cup coconut oil melted and cooled
  • 1 cup all-purpose flour
  • 1/2 cup vanilla whey protein powder about 2 scoops
  • 2 tsp pumpkin pie spice
  • 1 tsp baking soda
  • 1/2 tsp baking powder
  • 1/4 tsp salt

Equipment

  • 1 12-cup muffin tin
  • 1 Large Mixing Bowl
  • 1 Wire cooling rack

Instructions
 

  1. Preheat your oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease it well.
  2. In a large mixing bowl, whisk together the pumpkin puree, eggs, maple syrup, and melted coconut oil until smooth.
  3. Add the flour, protein powder, pumpkin pie spice, baking soda, baking powder, and salt to the wet ingredients.
  4. Gently fold the ingredients together with a spatula until just combined. Do not overmix. Fold in any optional add-ins like chocolate chips or nuts.
  5. Divide the batter evenly among the 12 muffin cups. Bake for 18-22 minutes, or until a toothpick inserted into the center comes out clean.
  6. Let the muffins cool in the tin for 5 minutes before transferring them to a wire rack to cool completely.

Notes

For best results, do not overmix the batter.
Store muffins in an airtight container at room temperature for up to 3 days.
Feel free to add 1/2 cup of chocolate chips or chopped nuts to the batter.

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