Pumpkin Muffins with Spiced Pepitas

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Pumpkin muffins, made with whole wheat pastry flour, feature spiced pepitas for a crunchy topping.

Pumpkin is one of my favorite flavors, and I don’t care whether it is the “correct” season to enjoy it.

After all, canned pumpkin is available year-round, and because I also freeze my own pumpkin puree, I can enjoy it whenever! Why limit it to only a few weeks of the year?

That means I frequently turn to pumpkin pancakes, chocolate pumpkin bundt cake, pumpkin gnocchi, and of course, pumpkin muffins.

pumpkin muffins with spiced pepitas topping on a wire cooling rack

These pumpkin muffins with pepitas are a bit different because they actually taste like pumpkin. 

Strange, I know, but most of the pumpkin baked goods I’ve tasted in recent years taste like cinnamon and cloves and sugar.

That’s fine sometimes, but when it comes to muffins I prefer to keep it a little less sweet.

I use whole wheat pastry flour for my pumpkin muffins, but you can use all-purpose flour if you prefer.

For a topping, I decided to use spiced pepitas to give the muffins crunch as well as a little bit of kick.

pumpkin muffins on a cooling rack

What are pepitas?

Pepitas are shelled pumpkin seeds. I actually didn’t know until a few years ago that the shell was a separate part of the pumpkin seed!

The shell is fine for snacking on when you’re roasting your jack o’lantern seeds, but pepitas are what you want for incorporating into other recipes.

Getting rid of the chewy exterior makes them so much more delicious and satisfying.

You can find pepitas at most grocery stores nowadays, either in the bulk bins or among the nuts and sunflower seeds. 

If you can’t find unsalted pepitas, just skip the salt in the seasoning blend.

These get sprinkled on top of the muffin batter before baking. You can also fold the spiced pepitas into the batter if you don’t have any picky eaters in the house. 

Don’t want to use pepitas? Sprinkle on some cinnamon sugar before baking.

tray of pumpkin muffins with a plaid napkin

Storage tips 

I love that this recipe uses a whole can of pumpkin. Not only do you not have to worry about leftover pumpkin, but it also ensures leftovers!

After all, it’s just as easy to make a big batch of muffins as it is a small one.

The recipe makes between 20 and 24 muffins, depending on how you fill your pan and the size of the muffin wells.

These are best warm from the pan, but you can also store them in an airtight container for up to 3 days.

You can freeze pumpkin muffins for longer storage!

Let the muffins cool completely, then transfer them into freezer-safe containers or bags.

I like to freeze them in packs of 4, and thaw each bag as needed in the refrigerator overnight.

You can also grab them straight from the freezer and pop them into the microwave for 15-30 seconds.

hand picking up a pumpkin muffin

Muffins are perfect for snacks because they are quick to prepare, are easy to store, and are pretty much endlessly customizable.

Pumpkin muffins are a great breakfast option, just like my pumpkin scones with white chocolate chips

Or just make sure to have them on hand next time your snacking hand goes a-wandering.

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It means so much when you enjoy my recipes, so let me know how it goes and leave a comment if you have any questions.

pumpkin muffins with spiced pepitas topping on a wire cooling rack

Pumpkin Muffins with Spiced Pepitas

These whole wheat pumpkin muffins with pepitas are full of autumnal flavor.
Author : Megan Myers
5 from 1 vote
Print Pin Recipe Review
Prep Time 15 minutes
Cook Time 25 minutes
Total Time 40 minutes
Servings 20
Calories 259 kcal


Spiced Pepitas

  • 2 teaspoons unsalted butter
  • ½ cup shelled pumpkin seeds, (pepitas)
  • ¼ teaspoon ground cinnamon
  • 1/3 teaspoon ground chipotle pepper
  • ¼ teaspoon cumin
  • Pinch salt
  • 1 tablespoon honey

Pumpkin Muffins

  • Nonstick cooking spray
  • 3 ½ cups whole wheat pastry flour, or all-purpose flour
  • 1 ½ teaspoons ground cinnamon
  • 1 teaspoon ground ginger
  • ¼ teaspoon ground cloves
  • 2 teaspoons baking powder
  • 1 teaspoon fine sea salt
  • ½ teaspoon baking soda
  • 15 ounces pumpkin puree, about 2 cups
  • 1 cup sugar
  • 3 large eggs
  • 1 ½ cups milk


For the Spiced Pepitas:

  • In a nonstick skillet, melt butter over medium heat. Add pumpkin seeds and stir to coat. Mix together cinnamon, chipotle, cumin, and salt, and sprinkle over pumpkin seeds. Stir well and cook for 2 minutes, until seeds start to get toasty.   
  • Stir in honey, and continue to cook for 2 more minutes. Pour seeds out onto wax paper, parchment paper, or a Silpat liner, and let cool.

For the Pumpkin Muffins:

  • Preheat oven to 375° F. Coat muffin cups with cooking spray or fill with paper liners; set aside.
  • In a large bowl, whisk together flour, cinnamon, baking powder, salt, and baking soda.
  • In a medium bowl, whisk together pumpkin and sugar. Whisk in eggs, one at a time, then the milk, until well combined.
  • Pour pumpkin mixture into flour mixture. Stir briskly, with a spatula, until batter is combined. Do not overmix. Fill each muffin cup with about 1/3 cup of the batter. Sprinkle each with the spiced pumpkin seeds.
  • Bake until a toothpick inserted into the center of the muffins comes out clean, about 18 minutes. Remove muffins from tins while still warm.


Serving: 1 muffinCalories: 259 kcalCarbohydrates: 48 gProtein: 9 gFat: 5 gSaturated Fat: 2 gCholesterol: 33 mgSodium: 235 mgFiber: 5 gSugar: 13 g

Nutrition information is provided as a courtesy and is an estimate based on online calculators. Any nutritional information found on Stetted should be used as a general guideline only.

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About Megan

I focus on fresh ingredients and easy methods, with spins that keep meals interesting. Dinnertime shouldn’t be stressful or complicated, and I’m here to help you enjoy the time spent in the kitchen. Read more…

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