Fall is here, and nothing says cozy season quite like pumpkin spice! If you’re looking for a snack that feels like a treat but is secretly packed with protein and wholesome ingredients, these Pumpkin Protein Muffins are about to be your new go-to.

I love these because they’re the perfect balance: sweet enough for kids to devour, but healthy enough that you won’t feel guilty enjoying one (or two!) yourself. Bonus—they’re easy to make, preservative-free, and fun to bake with the kids.

Ingredients You’ll Need

3 Tbsp melted coconut oil (or your favorite oil)
¼ cup packed brown sugar
¼ cup pure maple syrup
¼ cup unsweetened applesauce
¼ cup Greek yogurt (room temperature)
8 oz can pumpkin puree
2 large eggs
1 tsp pure vanilla extract
1 tsp baking powder
½ tsp fine salt
1 Tbsp pumpkin pie spice blend
½ cup vanilla protein powder (or unflavored – that’s what I had, and it worked perfectly!)
1 ¼ cup all-purpose flour

Step-by-Step Directions

Step 1: Prep the Oven and Muffin Tin

Preheat your oven to 350°F. Line a muffin tin with paper liners and lightly spray them with cooking spray so nothing sticks. (I used olive oil spray—it works like a charm!)

Step 2: Mix the Wet Ingredients

In a large mixing bowl, whisk together:

coconut oil
brown sugar
maple syrup
applesauce
Greek yogurt
pumpkin puree
eggs
vanilla extract

Whisk until smooth and creamy.

Step 3: Add the Dry Ingredients

Gently fold in:

baking powder
salt
pumpkin pie spice
protein powder
flour

Stir until everything is just combined. (Pro tip: I let my kids help with this part—they love stirring! I finish it off to make sure it’s not overmixed, which keeps the muffins fluffy and tender.)

Step 4: Fill the Muffin Cups

Use a ¼ cup measuring scoop or cookie scoop to evenly divide the batter among the muffin liners.

Step 5: Bake to Perfection

Bake for 20–23 minutes, or until a toothpick inserted in the center comes out clean.

Step 6: Cool & Enjoy

Let them cool in the pan for a few minutes before transferring them to a wire rack. Store in a glass container on your counter—they’ll be ready for after-school snacks or breakfast on the go.

Fun Twist for the Kids

We added Trader Joe’s sprinkles to the tops before baking for a fun Halloween vibe. The kids loved it! You could also toss in chocolate chips, chopped nuts, or even swirl a little cream cheese on top for a bakery-style feel.

Why You’ll Love These Muffins

Kid-approved: Sweet, soft, and pumpkin-y with just the right amount of spice.
Protein-packed: Thanks to Greek yogurt and protein powder, they keep you full longer.
No guilt: No preservatives, no junk—just wholesome ingredients you can feel good about.

Whether you’re packing them in lunchboxes, serving them with a cozy cup of coffee, or handing them out as an after-school snack, these pumpkin protein muffins are sure to be a hit in your house this fall.

Pumpkin Protein Muffins