Pumpkin Protein Muffins
These pumpkin protein muffins bring all the best fall flavors to breakfast! They’re soft, moist, and warmly spiced, with plenty of pumpkin and 7 grams of protein in every muffin. Add chocolate chips for the perfect finishing touch!
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A Note from Kim
A Lighter Take on a Fall Favorite
My pumpkin protein muffins have everything I love about classic pumpkin muffins, but in a better-for-you package. They have a nice boost of protein, less sugar and oil, and are naturally sweetened with maple syrup. I wanted them to have that same soft, moist texture and cozy pumpkin spice flavor, and Greek yogurt and pumpkin help make that happen.
They’re lightly sweet on their own, but I usually add chocolate chips because, in my opinion, pumpkin and chocolate are always a good idea! I also love adding a sprinkle of coarse sugar on top for that little bit of crunch you get with bakery-style muffins. And if you love adding more protein to your baked goods, try my banana protein muffins next!
With love (and lots of good eats), 
These pumpkin protein muffins turned out amazing! They’re soft, moist, and full of pumpkin spice flavor without being too sweet. I added mini chocolate chips and a sprinkle of coarse sugar on top, which made them even better. They baked up beautifully with tall, rounded tops, and you’d never guess they have protein powder in them.
— Kate
Everything You Need for Pumpkin Protein Muffins
Whip up a batch of these pumpkin protein muffins for an easy breakfast or grab-and-go snacks throughout the week. They’re a delicious way to sneak a little extra protein into something the whole family will love!
The full list of ingredients with measurements can be found in the printable recipe card below.
- Pumpkin puree: Adds plenty of pumpkin flavor and moisture for a soft, tender texture. Be sure to use 100% pure pumpkin, not pumpkin pie filling.
- Greek yogurt: Adds moisture and a boost of protein while helping create a soft texture. Plain or vanilla Greek yogurt both work well.
- Eggs: Give the batter structure and help everything bake up light and fluffy.
- Maple syrup: Naturally sweetens the recipe and pairs perfectly with pumpkin and warm fall spices.
- Avocado oil or melted butter: Adds moisture and richness. Avocado oil has a neutral flavor, while butter gives you a slightly richer taste.
- Vanilla extract: Enhances the sweetness and warm spice flavors.
- All-purpose flour: Provides structure. For the best results, weigh your flour or spoon and level it so you don’t accidentally use too much.
- Protein powder: Gives this recipe its protein boost! I used Truvani vanilla whey protein, and it worked really well. Different protein powders absorb liquid differently, so you may need a splash of milk if the batter seems too thick.
- Baking powder + baking soda: Work together to create a good rise and those beautiful, rounded tops.
- Spices: Cinnamon, ginger, nutmeg, and cloves add plenty of warm, cozy pumpkin spice flavor. Allspice can be used in place of the cloves.
- Salt: Balances the sweetness and helps bring out all the other flavors.
- Extras: Chocolate chips are great for a little more sweetness, while chopped pecans add crunch. I also love sprinkling turbinado sugar over the tops for a sweet, bakery-style finish.
Recipe Variations
- Skip the protein powder: Replace the ½ cup (50g) protein powder with ½ cup (60g) all-purpose flour. Since protein powder absorbs liquid differently than flour, the texture may vary slightly, but this will give you a more classic pumpkin muffin.
- Gluten-free option: Swap the all-purpose flour for a 1:1 gluten-free all-purpose flour blend. Be sure your protein powder is gluten free, too.
- Make mini muffins: Divide the batter between a greased or lined mini muffin pan. Bake at 350°F for about 10–13 minutes, or until the tops spring back when lightly touched and a toothpick comes out mostly clean. Skip the initial 425°F bake for minis since they cook so quickly.
- Try different mix-ins: Swap the chocolate chips for white chocolate chips, dried cranberries, or even cinnamon chips for a different fall flavor.
Kim’s Recipe Tips
- Whey works best: I had the best results with whey protein powder. Plant-based powders tend to absorb more moisture and may give you a denser or drier texture.
- Don’t overmix: Stir the dry ingredients into the wet just until everything is combined. Overmixing can make the texture tough instead of soft and tender.
- Fill the cups all the way: For those tall, rounded muffin tops, divide the batter evenly and fill each muffin cup completely full.
- Don’t overbake: Protein powder can dry out baked goods quickly. Start checking at 12 minutes after lowering the oven temperature. Mine were done right at that point.
How to Make Pumpkin Protein Muffins
I’ve included step-by-step photos below to make this recipe easy to follow at home. For the full printable recipe instructions and ingredient quantities, scroll to the recipe card at the bottom of this post.
Step 1: Whisk wet ingredients. In a large bowl, whisk together the pumpkin puree, Greek yogurt, eggs, maple syrup, avocado oil or melted butter, and vanilla until smooth.
Step 2: Mix dry ingredients. In a separate bowl, whisk together the flour, protein powder, baking powder, baking soda, salt, cinnamon, ginger, nutmeg, and cloves or allspice.
Step 3: Combine. Add the dry ingredients to the wet ingredients and gently stir until just combined. Don’t overmix.
Step 4: Stir add-ins. Fold in the chocolate chips and any other add-ins you might be using.
Step 5: Bake. Divide batter among muffin cups. Add toppings, if desired. Bake at 425°F for 5 minutes, then reduce to 350°F. Bake another 12–15 minutes, until tops are rounded and a toothpick comes out mostly clean.
Step 6: Cool. Let the muffins cool in the pan for about 5 minutes, then transfer them to a wire rack to cool completely.
How to Store and Freeze
- Store: Keep leftover pumpkin protein muffins in an airtight container at room temperature for up to 2 days or in the refrigerator for up to 5 days. Line the container with paper towels to absorb excess moisture.
- Freeze: Once completely cool, wrap each muffin individually and place in a freezer-safe bag or container. Freeze for up to 3 months.
- Reheat: Thaw overnight in the refrigerator or at room temperature. For that fresh-from-the-oven taste, warm in the microwave for 15–30 seconds. Frozen muffins may need 45–60 seconds.
Recommended Tools
- Mixing bowls: Any mixing bowls will work, but I love this nonslip set from Amazon. They stay put while you’re mixing!
- Nonstick muffin pan: A good muffin pan makes all the difference! I have this one from Williams Sonoma and absolutely love it. No paper liners needed, the muffins pop right out, and cleanup is a breeze.
- Cooling rack: Not essential, but definitely handy! A wire rack allows air to circulate so your muffins cool evenly without getting soggy on the bottom.
More Pumpkin Breakfast Recipes
If you try this pumpkin protein muffin recipe, let me know! Leave a comment and if you love it as much as I do, be sure to give it a five star ⭐️ rating! Also, subscribe to our mailing list to receive more delicious recipes straight to your inbox.
Pumpkin Protein Muffins
Ingredients
- 1 cup (240g) pumpkin puree
- ¾ cup (180g) plain or vanilla Greek yogurt
- 2 large eggs
- ¼ cup (80g) maple syrup
- 3 tablespoons (42g) avocado oil or melted butter
- 1 teaspoon vanilla extract
- 1½ cups (180g) all-purpose flour
- ½ cup (50g) vanilla or unflavored protein powder*
- 1 teaspoon baking powder
- ¾ teaspoon baking soda
- ½ teaspoon salt
- 2 teaspoons cinnamon
- ½ teaspoon ground ginger
- ¼ teaspoon nutmeg
- ⅛ teaspoon ground cloves or allspice
- Optional: ⅓ cup (55–60g) mini or regular chocolate chips, plus extras for the top if desired
- Optional: 1–1½ tablespoons (15–20g) turbinado sugar, for topping
- Optional: ¼–⅓ cup (30–40g) chopped pecans
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Instructions
- Preheat oven to 425°F. Line a 12-cup muffin pan with paper liners or lightly grease with nonstick spray.
- In a large bowl, whisk together the 1 cup (240g) pumpkin puree, ¾ cup (180g) plain or vanilla Greek yogurt, 2 large eggs, ¼ cup (80g) maple syrup, 3 tablespoons (42g) avocado oil or melted butter, and 1 teaspoon vanilla extract until smooth.
- In a separate bowl, whisk together the 1½ cups (180g) all-purpose flour, ½ cup (50g) vanilla or unflavored protein powder*, 1 teaspoon baking powder, ¾ teaspoon baking soda, ½ teaspoon salt, 2 teaspoons cinnamon, ½ teaspoon ground ginger, ¼ teaspoon nutmeg, and ⅛ teaspoon ground cloves or allspice.
- Add the dry ingredients to the wet ingredients and gently stir until just combined. Don't overmix. Fold in the optional ⅓ cup (55–60g) mini or regular chocolate chips, if using.
- Divide the batter evenly among the muffin cups, filling each completely full. Sprinkle the tops with turbinado sugar, extra chocolate chips and chopped pecans, if using.
- Bake at 425°F for 5 minutes, then, without opening the oven, reduce the temperature to 350°F and bake for another 12–15 minutes, or until the tops are rounded and a toothpick inserted in the center comes out mostly clean. Check at the 12 minute mark (mine were done).
- Let the muffins cool in the pan for about 5 minutes, then transfer them to a wire rack to cool completely.
Notes
Did you make this recipe?
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My husband had no idea these were protein muffins! He ate two before I even told him.
Made these for meal prep and they’re such an easy grab-and-go breakfast. I’ll definitely make another batch.
These pumpkin protein muffins turned out amazing! They’re soft, moist, and full of pumpkin spice flavor without being too sweet. I added mini chocolate chips and a sprinkle of coarse sugar on top, which made them even better. They baked up beautifully with tall, rounded tops, and you’d never guess they have protein powder in them.
The maple syrup gives them just enough sweetness. I added pecans on top and loved the crunch.
The texture is incredible! I followed the recipe exactly and they came out tall, fluffy, and moist.
I made these for breakfast this week and loved them. They stayed moist for several days too!
These were delicious! I used the turbinado sugar and pecans on top, and they tasted like something from a bakery.
These turned out beautifully! The high oven temperature at the beginning gave mine the prettiest rounded tops.
I’ve tried a few protein muffin recipes that turned out dry, but these were actually really moist and fluffy!
So happy to hear!
So good! You’d never guess these have protein powder in them. The texture was just like a regular pumpkin muffin.
These turned out so soft and moist! I added chocolate chips, and my whole family loved them.
These might be the best protein muffins I’ve made. They didn’t have that dry, chalky texture that protein baked goods sometimes have.
Made these today and they are delicious!! I followed the recipe exactly and they came out so moist. I used and protein powder specifically for baking and am so excited I now have a recipe to use for it.
So, so glad you enjoyed and thanks so much for taking the time to comment!!
Finally a protein muffin that actually tastes like a muffin! Soft, moist, and so much pumpkin flavor.
I can’t wait to try these!
I made These Tonight And they came out so good. Only sub I made was using plain Greek yogurt and added walnuts! I will definitely be making these again 🙂
That’s awesome!! I’m so glad that you loved them!
I LOVE these! A pumpkin treat that I don’t even have to tell myself is a treat. They are pure perfection!
Awwww…. thanks, girl!!