These pumpkin protein muffins are the perfect solution for a quick, healthy breakfast or a satisfying post-workout snack. They are incredibly moist, packed with warm fall spices, and loaded with protein to keep you full and energized throughout the day. Forget dry, bland protein baked goods; this recipe guarantees a deliciously fluffy texture and rich pumpkin flavor in every single bite. We’ve crafted this recipe to be simple, using pantry staples alongside your favorite protein powder for a treat you can feel good about.
Whether you’re looking for a nutritious meal prep option or a healthier way to satisfy your sweet tooth, these muffins are the answer. They come together in one bowl and are ready in under 30 minutes, making them a go-to for busy mornings.

Why You’ll Love These Pumpkin Protein Muffins
- High in Protein: Each muffin provides a significant protein boost, perfect for starting your day or refueling after exercise. This makes them a great component of many high-protein meal plans.
- Incredibly Moist: We use a combination of pumpkin puree and Greek yogurt to ensure these muffins are never dry, a common issue with protein baking. The result is a tender, super-moist crumb.
- Easy One-Bowl Recipe: Minimal mess and simple steps mean you can whip up a batch in no time. Just mix the wet ingredients, then the dry, and bake!
- Perfect for Meal Prep: These muffins store beautifully, making them an ideal grab-and-go breakfast or snack for the entire week.
Key Ingredients for the Perfect Muffins
This recipe uses simple, wholesome ingredients to create the best pumpkin protein muffins. Here’s what you’ll need:
For the Muffins:
- Pumpkin Puree: The star of the show! Use 100% pure pumpkin puree, not pumpkin pie filling, for authentic flavor and moisture.
- Protein Powder: Vanilla or unflavored whey or casein blend works best. The type of protein powder can affect texture, so stick to a brand you know works well in baking.
- Flour: We use a mix of all-purpose and whole wheat flour for a perfect balance of texture and nutrition. You can also use oat flour for a gluten-free option.
- Greek Yogurt: This is our secret weapon for an ultra-moist and tender muffin while adding an extra protein kick.
- Sweetener: Maple syrup adds natural sweetness and a hint of classic fall flavor.
- Eggs: To bind the ingredients and provide structure.
- Spices: A classic blend of cinnamon, nutmeg, ginger, and cloves creates that cozy pumpkin spice flavor.
- Leavening Agents: Baking soda and baking powder help the muffins rise and become light and fluffy.

Step-by-Step Instructions
Making these pumpkin protein muffins is incredibly simple. 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 lightly grease it.
- Mix Wet Ingredients: In a large bowl, whisk together the pumpkin puree, eggs, Greek yogurt, and maple syrup until smooth and well combined.
- Combine Dry Ingredients: In a separate bowl, stir together the all-purpose flour, whole wheat flour, protein powder, baking soda, baking powder, and all the spices.
- Combine 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 distribute the batter among the 12 muffin cups, filling each about three-quarters full.
- Bake to Perfection: Bake for 18-22 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.
Tips for Success and Variations
Expert Tips
- Don’t Overmix: Overmixing the batter develops gluten, which can lead to tough, dense muffins. Mix only until the flour is no longer visible.
- Protein Powder Matters: Different protein powders absorb liquid differently. A whey-casein blend is often recommended for baking as it helps retain moisture.
- Check for Doneness: Ovens can vary. Start checking your muffins at the 18-minute mark to avoid overbaking.
Flavor Variations
- Add Chocolate Chips: Fold in a half cup of dark chocolate chips for a decadent treat. It’s a simple addition, much like in this classic chocolate chip cookie recipe.
- Nutty Crunch: Add a half cup of chopped walnuts or pecans to the batter for extra texture and healthy fats.
- Streusel Topping: For an extra special touch, top the muffins with a simple cinnamon-oat streusel before baking.
Storage and Freezing Instructions
These pumpkin protein muffins are perfect for making ahead. To store, 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 muffin individually in plastic wrap and place them in a freezer-safe bag. They will keep in the freezer for up to 3 months. Simply thaw at room temperature or warm in the microwave for a few seconds before enjoying. This makes them as convenient as our other make-ahead favorites, like these Greek yogurt banana muffins.
Frequently Asked Questions
Yes, absolutely. To make them gluten-free, simply replace the all-purpose and whole wheat flour with 1.5 cups of a high-quality, all-purpose gluten-free baking flour blend or use oat flour.
A whey and casein blend typically works best for baking as it helps retain moisture, resulting in a less dry muffin. However, a quality whey isolate or a plant-based protein powder can also be used, though you may need to slightly adjust the wet ingredients.
Store the 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.
Yes, you can substitute the eggs with a flax egg. For each egg, mix one tablespoon of ground flaxseed with three tablespoons of water and let it sit for about 5-10 minutes to thicken before adding it to the batter.
Based on the ingredients used in this recipe, each muffin contains approximately 155 calories and 10 grams of protein. Please note that this is an estimate and can vary based on the specific ingredients you use, such as the type of protein powder.
The Perfect Healthy Pumpkin Treat
These pumpkin protein muffins are the ultimate way to enjoy the flavors of fall without compromising your health goals. They are simple to make, packed with wholesome ingredients, and incredibly satisfying. Give this recipe a try and share your beautiful creations on Pinterest!

Pumpkin Protein Muffins

Pumpkin Protein Muffins: The Ultimate Healthy & Delicious Recipe
Ingredients
Equipment
Method
- Preheat your oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners or grease it.
- In a large mixing bowl, whisk together the pumpkin puree, eggs, Greek yogurt, and maple syrup until the mixture is smooth.
- In a separate, medium bowl, combine the all-purpose flour, whole wheat flour, vanilla protein powder, baking soda, baking powder, cinnamon, nutmeg, ginger, and cloves.
- Pour the dry ingredients into the wet ingredients. Use a spatula to gently fold them together until just combined. Do not overmix.
- Divide the batter evenly among the 12 prepared muffin cups.
- Bake for 18-22 minutes, or until a toothpick inserted into the center comes out clean.
- Allow the muffins to cool in the tin for 5 minutes before transferring them to a wire rack to cool completely.
Nutrition
Notes
For a gluten-free version, substitute the all-purpose and whole wheat flour with 1.5 cups of a gluten-free all-purpose baking blend or oat flour.
Feel free to add 1/2 cup of chocolate chips or chopped nuts to the batter for extra flavor and texture.












