Pumpkin Protein Muffins

Name: Pumpkin Protein Muffins
Prep time: 5 min
Cook time: 20 min
Total time: 25 min
Yield: 12
Cuisine: American
Ingredients: 1 cup pumpkin puree; 3 large eggs; ¼ cup maple syrup; ¼ cup oil; 1 teaspoon vanilla extract; 1 ½ cups oat flour; ½ cup vanilla protein powder; 2 teaspoons pumpkin pie spice; 1 teaspoon baking powder; ½ teaspoon baking soda; ½ teaspoon sea salt; ½ cup chocolate chips, optional

These pumpkin protein muffins are soft, fluffy, and packed with pumpkin spice flavor. They’re easy to make and bake up beautifully every time. Made with real pumpkin, protein powder, and a touch of maple syrup, they’re naturally sweetened and great for meal prep!

A cooling rack with a dozen baked protein pumpkin muffins cooling and a cup of coffee on the counter.

Pumpkin season is officially here, and I’m finding every excuse to work it into our weekly meal prep. I’ve been making my protein banana muffins for years, but these pumpkin protein muffins are the fall staple.

I always pack homemade muffins in my kids’ lunches because they’re easy to make ahead and hold up well. Kind of like a sweet treat, especially when made with chocolate chips.

And the texture? SO good. They’re soft, fluffy, and full of warm pumpkin spice flavor, with little pockets of melted chocolate in every bite. You’d never guess there’s protein powder in them! I highly recommend making a double batch and freezing the extras. You’ll be VERY thankful you did when you’re packing lunches at 7 am. I speak from experience.

Looking for more easy protein snacks? Check out my pumpkin protein balls or my favorite homemade protein bars.

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Ingredients

Pumpkin puree: Make sure to grab 100% pure pumpkin puree, not pumpkin pie filling, which contains added sugar and spices.

Maple syrup: Use pure maple syrup for natural sweetness and a hint of maple flavor.
Oil: I recommend avocado oil or melted coconut oil. If using coconut oil, make sure your eggs are at room temperature so the oil doesn’t solidify when mixed.
Oat flour: For best results, use store bought oat flour. Make sure to purchase certified gluten free oat flour if you need the muffins to be gluten free. While oats are gluten free, they can become contaminated with gluten in processing facilities.
Vanilla protein powder: Whey protein produces the softest, fluffiest muffins. Grass-fed beef or plant-based protein powder can also work, but may produce a denser texture.
Pumpkin pie spice: Grab a premade blend at the store. It’s easy to use and provides the perfect warm pumpkin spice!
Chocolate chips: I love using dark or semisweet chocolate chips, but feel free to leave them out or swap them for your favorite mix-ins.

See the recipe card for full information on ingredients and quantities.

Substitutions

Make it egg-free: Replace each egg with one flax egg. I’ve used flax eggs successfully in many baked goods, including muffins, cakes, and breads!
Maple syrup: Honey works as a 1:1 substitute for maple syrup. Keep in mind it may add a slightly different flavor.
Pumpkin pie spice: For every 1 teaspoon pumpkin pie spice, you can swap it for 1/2 teaspoon cinnamon + 1/4 teaspoon ground ginger + 1/4 teaspoon nutmeg.
Chocolate chips: Swap them for chopped pecans, walnuts, dried cranberries, or white chocolate chips. You can also leave them out entirely.

How to Make Pumpkin Protein Muffins

How to make the recipe, including mixing the wet ingredients, adding the flour and chocolate chips, pouring the batter into the muffin cups, and baking the pumpkin protein muffins.

Prep: Preheat the oven to 350°F. Line a muffin tin with parchment paper liners. Spray the liners with nonstick spray.
Mix: In a medium bowl, mix together the pumpkin puree, large eggs, maple syrup, oil, and vanilla extract.
Combine: In a separate bowl, whisk together the oat flour, protein powder, pumpkin pie spice, baking powder, baking soda, and sea salt until evenly combined. Slowly add the flour mixture to the wet ingredients. Mix until evenly combined and no clumps remain. Fold in the chocolate chips.
Transfer: Pour the batter into the muffin liners, filling each about ¾ full. I like to use a large cookie scoop to make this easier. Add a few extra chocolate chips on top if desired.
Bake: Bake in the center of the oven for 17-20 minutes until a toothpick comes out clean or the centers bounce back when lightly pressed. Transfer to a wire rack to cool completely before serving.

A stunning close up of a muffin with big chocolate chips on top.

Mix-ins

Even with the added protein powder, these muffins taste JUST like your favorite pumpkin muffins! Chocolate chips are my personal favorite mix-in, but you can easily switch things up. Just use ½ cup per batch. Here are a few ideas:

Chopped walnuts or pecans for a little crunch
Dark or semisweet chocolate chips
Dried cranberries or raisins
White chocolate chips for a sweeter twist
Topping only: Add a sprinkle of sliced almonds or pumpkin seeds on top just before baking.

Recipe Tips

Measure correctly. Oat flour can zap moisture, and if you use too much, it can make your muffins dry. To measure, spoon the flour into your measuring cup and level it off with a knife.
Don’t overmix. Stir the wet and dry ingredients together just until everything is incorporated. Overmixing can affect the texture of the finished muffins.
Use pumpkin puree, not pumpkin pie filling. Pure pumpkin gives these muffins their delicious flavor and moisture without added sugar or spices.
Don’t overbake! Protein powder can dry out baked goods when they’re cooked too long. Start checking the muffins around 17 minutes. The tops should spring back when lightly pressed, and a toothpick should come out with a few moist crumbs.
Let them cool before serving. Give the muffins a few minutes to set in the pan, then transfer them to a wire rack. This helps the texture set and keeps the bottoms from getting soggy.

FAQs

How do I know when muffins are done?

The tops should be lightly golden and spring back when gently pressed. If you need a visual—a toothpick inserted into the center should come out with just a few moist crumbs.

Are these muffins healthy?

I think so! These muffins are made with wholesome ingredients like pumpkin puree, oat flour, eggs, and protein powder. They’re naturally sweetened with maple syrup and provide more protein than traditional pumpkin muffins.

Why did my muffins turn out dense?

This can happen for a few reasons: 1.) Overmixing the batter, 2.) measuring too much oat flour, or 3.) using a protein powder that absorbs a lot of moisture. When making the muffins, spoon and level your oat flour, stir just until combined, and use whey protein powder if possible.

What kind of protein powder works best?

Whey protein generally produces the softest, fluffiest muffins. Plant-based and grass-fed beef protein powders also work, but you may notice a slightly denser texture depending on the brand. I don’t recommend substituting collagen peptides for the protein powder, as it doesn’t provide the same structure in baked goods.

Two muffins stacked on top of each other, with the top one having a bite taken out of it.

Storage

STORE: Once the pumpkin protein muffins have cooled completely, transfer them to an airtight container. They’ll stay fresh at room temperature for up to 3 days or in the refrigerator for up to a week.

FREEZE: These muffins freeze beautifully, so they’re perfect for meal prep! I love making a double batch so I always have snacks on hand for the kids. Just let the muffins cool and place them in a freezer-safe storage bag. They’ll keep in the freezer for up to 2 months.

THAW: When you’re ready to enjoy one, let it thaw at room temperature for about an hour or pop it in the microwave for 20–30 seconds until warmed through. You can also transfer frozen muffins to the fridge overnight so they’re ready for breakfast the next morning.

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