Start your day or refuel after a workout with a treat that’s as delicious as it is nutritious. These Healthy Pumpkin Protein Muffins are the perfect way to enjoy the cozy flavors of fall while getting a serious boost of protein and fiber. Made with whole wheat flour, protein powder, Greek yogurt, and real pumpkin puree, these muffins are moist, fluffy, and perfectly spiced. They are an ideal grab-and-go breakfast or a satisfying snack to power you through your day.
Why This is Your New Go-To Healthy Muffin
This recipe perfectly balances flavor and nutrition. Here’s why you’ll love it:
- Packed with Protein: With both protein powder and Greek yogurt, these muffins will help keep you feeling full and satisfied for hours.
- Made with Wholesome Ingredients: This recipe uses whole wheat pastry flour for added fiber and is naturally sweetened with coconut or brown sugar.
- Incredibly Moist & Fluffy: The combination of pumpkin puree, oil, and Greek yogurt ensures a wonderfully moist and tender muffin, never dry or chalky.
- Perfect for Meal Prep: Bake a batch on Sunday to have a healthy, pre-portioned snack ready for the entire week.
Your Wholesome Ingredient Checklist
This recipe uses a blend of nutritious ingredients to create a delicious and satisfying muffin.
Dry Ingredients:
- 1 ¼ cups whole wheat pastry flour
- ½ cup protein powder (plain or vanilla works best)
- 2 tsp cinnamon
- 1 ½ tsp baking soda
- ½ tsp ground ginger
- ½ tsp ground nutmeg
- ¼ tsp ground cloves
Wet Ingredients:
- 1 (15 oz) can pumpkin puree (not pumpkin pie filling)
- ¾ cup coconut sugar or packed brown sugar
- 2 large eggs
- ¼ cup avocado oil (or other neutral oil)
- ¼ cup plain Greek yogurt
- 2 tsp vanilla extract
Optional Add-in:
- ½ cup mini chocolate chips (plus more for topping)
Step-by-Step Guide to Healthy Muffins
Follow these simple steps for a perfect batch of protein-packed treats.
Part 1: Mix the Batter
- Preheat and Prep: Preheat your oven to 375°F (190°C). Line a standard 12-cup muffin tin with paper liners.
- Combine Dry Ingredients: In a medium bowl, whisk together the whole wheat pastry flour, protein powder, cinnamon, baking soda, ginger, nutmeg, and cloves. Set it aside.
- Combine Wet Ingredients: In a separate large bowl, whisk together the pumpkin puree, coconut sugar (or brown sugar), eggs, oil, Greek yogurt, and vanilla extract. Whisk until the mixture is smooth and no clumps of yogurt remain.
- Mix Wet and Dry: Pour the dry ingredients into the bowl with the wet ingredients. Use a spatula to stir everything together until just combined. Be careful not to overmix the batter.
- Fold in Chocolate Chips: If you’re using them, gently fold in the ½ cup of mini chocolate chips.
Part 2: Bake the Muffins
- Fill Muffin Cups: Divide the batter evenly among the 12 prepared muffin cups. They will be quite full.
- Add Topping (Optional): Sprinkle a few more mini chocolate chips on top of each muffin before baking.
- Bake: Place the muffin tin in the preheated oven and bake for 20-22 minutes. The muffins are done when a toothpick inserted into the center comes out clean.
- Cool and Enjoy: Let the muffins cool in the pan for a few minutes before transferring them to a wire rack to cool completely.
Tips for the Best Protein Muffins
- Choosing Your Protein Powder: A whey/casein blend or a plant-based protein powder will work well here. Vanilla-flavored powder is a great choice as it complements the other flavors, but plain will also work perfectly.
- Don’t Overmix: This is especially important when working with whole wheat flour and protein powder. Mix only until you no longer see streaks of dry flour to ensure the muffins stay tender and not tough.
- Whole Wheat Pastry Flour: This type of flour has a finer texture than regular whole wheat flour, which helps create a lighter, fluffier muffin. If you can’t find it, regular whole wheat or all-purpose flour can be used.
- Storage: 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 beautifully for a quick future snack.
Healthy Pumpkin Protein Muffins
These Healthy Pumpkin Protein Muffins are moist, fluffy, and packed with warm fall spices — plus a boost of protein from Greek yogurt and protein powder. Perfect for breakfast, a post-workout snack, or meal prep.
Equipment
- 12-cup muffin tin
- paper liners
- medium mixing bowl
- Large mixing bowl
- Whisk
- Spatula
- Wire Cooling Rack
Ingredients
- 1 1/4 cups whole wheat pastry flour
- 1/2 cup protein powder (plain or vanilla)
- 2 tsp ground cinnamon
- 1 1/2 tsp baking soda
- 1/2 tsp ground ginger
- 1/2 tsp ground nutmeg
- 1/4 tsp ground cloves
- 15 oz pumpkin puree (not pie filling)
- 3/4 cup coconut sugar or packed brown sugar
- 2 large eggs
- 1/4 cup avocado oil (or other neutral oil)
- 1/4 cup plain Greek yogurt
- 2 tsp vanilla extract
- 1/2 cup mini chocolate chips (optional, plus more for topping)
Instructions
- Preheat oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners.
- In a medium bowl, whisk together whole wheat pastry flour, protein powder, cinnamon, baking soda, ginger, nutmeg, and cloves.
- In a large bowl, whisk together pumpkin puree, coconut sugar, eggs, oil, Greek yogurt, and vanilla extract until smooth.
- Add dry ingredients to wet ingredients. Stir gently with a spatula until just combined. Do not overmix.
- Fold in mini chocolate chips if using.
- Divide batter evenly among muffin cups, filling nearly to the top. Sprinkle extra chocolate chips on top if desired.
- Bake for 20-22 minutes, or until a toothpick inserted into the center comes out clean.
- Cool in the pan for a few minutes, then transfer to a wire rack to cool completely.
Notes
Use whole wheat pastry flour for the lightest texture, and avoid overmixing to keep the muffins tender. Store in an airtight container at room temperature for up to 3 days, in the fridge for up to a week, or freeze for up to 3 months.