Pumpkin Protein Muffins Recipe
If you’re on the hunt for a snack that combines wholesome nutrition with cozy, autumnal flavors, look no further than these Pumpkin Protein Muffins. They are a delectable blend of moist pumpkin puree, fragrant spices, and the perfect boost of protein to keep you energized. Whether you need a quick breakfast on the go or a nourishing afternoon pick-me-up, these muffins strike a balance between indulgent and healthy in the most delightful way. Once you try them, you’ll see why Pumpkin Protein Muffins have quickly become a favorite in my kitchen and one I’m excited to share with you!

Ingredients You’ll Need
These ingredients come together effortlessly, each playing a vital role in delivering the perfect taste, texture, and nutrition. From the whole wheat pastry flour that adds a tender crumb to the warm spices that give these muffins their signature pumpkin flavor, every component is essential for success.
- Whole wheat pastry flour: Provides a light, tender base while adding nutritional fiber and depth.
- Protein powder (plain, vanilla, or chocolate): Boosts the protein content, supporting muscle recovery and satiety.
- Cinnamon: Adds comforting warmth and a hint of natural sweetness.
- Baking soda: Ensures the muffins rise beautifully and have a light texture.
- Ground ginger: Brings a subtle, zesty spice that complements pumpkin perfectly.
- Ground nutmeg: Enhances the cozy, earthy flavors of the pumpkin.
- Ground cloves: Offers a rich, aromatic note that rounds out the spice mix.
- Canned pumpkin puree (not pumpkin pie filling): The star ingredient that keeps muffins moist and packed with vitamin A.
- Coconut sugar or brown sugar: Sweetens naturally with a subtle caramel undertone.
- Eggs: Bind everything together and contribute to the tender crumb.
- Avocado oil: Adds healthy fat while keeping the muffins moist without a strong taste.
- Plain Greek yogurt: Keeps the texture rich and adds protein and tang.
- Vanilla extract: Enhances the overall flavor profile with its sweet, aromatic note.
- Mini chocolate chips (optional): A little indulgence that melts into pockets of melty goodness.
How to Make Pumpkin Protein Muffins
Step 1: Preheat and Prepare
First off, get your oven warmed to 375°F and line your 12-muffin tin with paper liners or lightly grease it. This step ensures your muffins cook evenly and come out cleanly from the tin once baked.
Step 2: Combine Dry Ingredients
In a medium bowl, whisk together the whole wheat pastry flour, protein powder, cinnamon, ginger, nutmeg, cloves, and baking soda. Mixing these dry ingredients now means the spices and leavening agents are evenly distributed, crucial for consistent flavor and lift in every bite.
Step 3: Whisk Wet Ingredients
In a separate larger bowl, combine the pumpkin puree, coconut sugar, eggs, avocado oil, Greek yogurt, and vanilla extract. Beat this mixture until smooth and homogenous, making sure no lumps of yogurt remain. This mixture will bring moisture and richness, giving your muffins their signature tender crumb.
Step 4: Bring It All Together
Add the dry ingredients to the wet and gently stir until just combined. Avoid overmixing here to keep your muffins soft and fluffy. If you’re including mini chocolate chips, fold them in now for melty, chocolatey surprises.
Step 5: Fill and Bake
Divide the batter evenly among the muffin cups. For a pretty finish and a bit more chocolate flavor, sprinkle a few mini chocolate chips on top of each muffin. Pop the tin into your preheated oven and bake for 20 to 22 minutes. You’ll know they’re done when a toothpick inserted in the center comes out clean.
Step 6: Cool and Enjoy
Once baked, allow your Pumpkin Protein Muffins to cool in the tin for a few minutes before transferring them to a wire rack. This helps prevent sogginess and keeps the edges perfectly tender. Then, dive in and enjoy!
How to Serve Pumpkin Protein Muffins

Garnishes
Enhance your Pumpkin Protein Muffins by adding a light spread of nut butter or a drizzle of honey right before serving. A dusting of powdered cinnamon or a thin swipe of cream cheese frosting can also jumpstart the cozy factor even more.
Side Dishes
These muffins pair wonderfully with a warm cup of chai tea or your morning coffee for a balanced breakfast. For a fuller meal, consider serving alongside fresh fruit or a simple green smoothie to keep the protein theme going strong.
Creative Ways to Present
If you’re sharing at a brunch or gathering, set up a toppings bar with options like crushed nuts, shredded coconut, or even yogurt parfait layers. Pumpkin Protein Muffins also taste amazing sliced in half and toasted for a quick protein-packed snack anytime.
Make Ahead and Storage
Storing Leftovers
Store your Pumpkin Protein Muffins in an airtight container at room temperature for up to three days. This keeps them fresh and moist without drying out, making them perfect for quick grabs throughout the week.
Freezing
If you want to enjoy these muffins longer, freeze them individually wrapped in plastic and placed in a freezer-safe bag for up to three months. When it’s muffin time, just thaw at room temperature or warm them up gently.
Reheating
Reheat refrigerated or thawed Pumpkin Protein Muffins in a microwave for about 15 seconds or until warmed through. You can also pop them in a toaster oven to regain a slightly crisp top and soft center, just like fresh-baked.
FAQs
Can I use a different flour?
Absolutely! While whole wheat pastry flour gives a tender and wholesome texture, you can substitute with all-purpose flour or oat flour. Just keep in mind the texture might shift slightly, with oat flour adding a heartier bite.
Is protein powder necessary?
Protein powder adds that extra boost, but you can omit it if you prefer. Your muffins will still be delicious and moist, just with a bit less protein content.
Can I make these muffins gluten-free?
Yes, using a gluten-free flour blend works well. Make sure the blend is suitable for baking and contains xanthan gum or a similar binder to help with texture.
Are mini chocolate chips optional?
Definitely optional! They add a fun melty surprise, but you can leave them out for a simpler flavor or swap for chopped nuts for added crunch instead.
How spicy are these muffins?
The spice blend is warm and cozy without being overpowering, perfect for those who enjoy subtle pumpkin spice flavor. You can adjust the amounts of cinnamon or ginger to suit your taste.
Final Thoughts
I can’t recommend these Pumpkin Protein Muffins enough — they’re a perfect way to enjoy the flavors of fall with a nutritious twist. Whether you’re meal prepping or treating yourself, these muffins deliver a delicious and wholesome punch every single time. Grab your ingredients, give this recipe a whirl, and get ready to fall in love with Pumpkin Protein Muffins all over again.
PrintPumpkin Protein Muffins Recipe
These Pumpkin Protein Muffins are a deliciously moist and flavorful treat packed with wholesome ingredients like whole wheat pastry flour, protein powder, and pumpkin puree. Perfect for a nutritious breakfast or snack, they are lightly spiced with warm cinnamon, ginger, nutmeg, and cloves, and optionally studded with mini chocolate chips for a subtle sweetness.
- Prep Time: 10 minutes
- Cook Time: 20-22 minutes
- Total Time: 30-32 minutes
- Yield: 12 muffins 1x
- Category: Breakfast, Snack, Dessert
- Method: Baking
- Cuisine: American
- Diet: Low Fat
Ingredients
Dry Ingredients
- 1 ¼ cups whole wheat pastry flour
- ½ cup protein powder (plain, vanilla, or chocolate)
- 2 tsp cinnamon
- 1 ½ tsp baking soda
- ½ tsp ground ginger
- ½ tsp ground nutmeg
- ¼ tsp ground cloves
Wet Ingredients
- 15 oz canned pumpkin puree (not pumpkin pie filling)
- ¾ cup coconut sugar or brown sugar
- 2 large eggs
- ¼ cup avocado oil
- ¼ cup plain Greek yogurt
- 2 tsp vanilla extract
Add-ins (Optional)
- ½ cup mini chocolate chips plus more for topping
Instructions
- Preheat Oven and Prepare Pan: Preheat your oven to 375°F (190°C) and line a 12-count muffin tin with paper liners or lightly grease the pan.
- Mix Dry Ingredients: In a medium bowl, whisk together the whole wheat pastry flour, protein powder, cinnamon, ground ginger, nutmeg, cloves, and baking soda until evenly combined. Set aside.
- Combine Wet Ingredients: In a separate large bowl, whisk the pumpkin puree, coconut sugar (or brown sugar), eggs, avocado oil, Greek yogurt, and vanilla extract together until the mixture is smooth and no yogurt clumps remain.
- Incorporate Dry into Wet: Add the dry ingredient mixture into the wet ingredients bowl and gently stir until just combined; do not overmix to keep muffins tender.
- Add Chocolate Chips: Fold in the mini chocolate chips if using, reserving some to sprinkle on top of the muffins.
- Fill Muffin Tin: Divide the batter evenly among the 12 muffin cups. Sprinkle the remaining mini chocolate chips on top of each muffin for a decorative and tasty finish.
- Bake: Bake in the preheated oven for 20 to 22 minutes, or until a toothpick inserted into the center of a muffin comes out clean or with a few moist crumbs.
- Cool and Serve: Remove the muffins from the oven and allow them to cool in the pan for 5 minutes before transferring them to a wire rack to cool completely. Serve warm or at room temperature.
Notes
- You can substitute the protein powder with your preferred type (whey, plant-based, etc.), but keep the amount consistent.
- Using Greek yogurt adds protein and moisture; full-fat yogurt yields richer muffins while low-fat options reduce calories.
- Coconut sugar provides a mild caramel flavor; brown sugar can be used as a direct substitute.
- The mini chocolate chips are optional and can be omitted for a dairy-free or lower-sugar version.
- Store muffins in an airtight container at room temperature for up to 3 days or refrigerate for up to a week.
- These muffins freeze well; wrap individually and freeze for up to 3 months.
Nutrition
- Serving Size: 1 muffin
- Calories: 180
- Sugar: 9g
- Sodium: 150mg
- Fat: 7g
- Saturated Fat: 1g
- Unsaturated Fat: 6g
- Trans Fat: 0g
- Carbohydrates: 22g
- Fiber: 3g
- Protein: 8g
- Cholesterol: 40mg
Keywords: Pumpkin protein muffins, healthy pumpkin muffins, protein breakfast muffins, pumpkin snack, whole wheat muffins