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eight pumpkin muffins with cream cheese fillings are sitting on a wire rack on top of a light aqua colored napkin.

Pumpkin Cream Cheese Muffins

Course: Bread, Breakfast, Brunch, Dessert
Cuisine: American
Keyword: pumpkin cream cheese muffins, starbucks pumpkin cream cheese muffin
Servings: 14
Calories: 236kcal
These amazing Pumpkin Cream Cheese Muffins are the perfect fall treat! These perfectly moist pumpkin muffins are filled with a creamy, luscious cream cheese filling and topped with sweetened and spiced pumpkin seeds. A delicious addition to your brunch (or dessert!) menu this holiday season.
Print Recipe


Pumpkin Muffins

  • 1 cup pumpkin puree
  • cup vegetable oil
  • ½ cup brown sugar
  • ½ cup granulated sugar
  • ¼ cup whole milk
  • 2 large eggs
  • 1 teaspoon vanilla extract or vanilla bean paste
  • 2 cups all purpose flour
  • 2 teaspoons pumpkin pie spice
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • ¼ teaspoon salt

Cream Cheese Filling

  • 8 ounces cream cheese softened slightly
  • 1 tablespoon all purpose flour
  • ½ cup granulated sugar
  • 1 teaspoon sour cream
  • 1 teaspoon vanilla extract or vanilla bean paste
  • ½ teaspoon sea salt or kosher salt


  • ¼ cup pumpkin seeds
  • 1 teaspoon pumpkin pie spice
  • ¼ teaspoon granulated sugar


For the Pumpkin Muffins:

  • Preheat the oven to 375°F and line a muffin pan with parchment liners. If not using parchment, spray liners with a nonstick cooking spray. Set aside.
  • In a large bowl, whisk together the vegetable oil and pumpkin puree. Add the brown sugar and granulated sugar and whisk to combine. Next, whisk in the milk, eggs and vanilla extract. Set aside.
  • In a medium bowl, whisk together the all purpose flour, pumpkin pie spice, baking powder, baking soda and salt.
  • Fold the dry ingredients into the wet pumpkin mixture and stir just until combined.
  • Scoop the batter into the prepared muffin pan almost to the top.
  • With a spoon or knife, press a hole or indentation into the batter of each muffin, making way for the cream cheese filling.

For the Cream Cheese Center:

  • In a large bowl or the bowl of a stand mixer, add the cream cheese and beat until creamy.
  • Add the flour, granulated sugar, sour cream, vanilla extract and salt and continue beating until fully combined.
  • Transfer the cream cheese mixture into a large resealable bag and press the mixture into one corner. Cut one corner off the bottom of the bag and fill the centers of each muffin with the cream cheese filling.

Spiced Pumpkin Seeds:

  • In a small bowl, toss the pumpkin seeds together with the pumpkin pie spice and sugar.
  • Top each muffin with a few of the pumpkin seeds.
  • Bake for 18 to 22 minutes. Insert a toothpick into the pumpkin part of the muffin. It should come out clean with a few moist crumbs. Don’t insert it into the cream cheese filling.
  • Let muffins cool for 10 minutes in the muffin pan before transferring to a cooling rack.


Storage Information

Leftovers can be stored in the refrigerator for up to 5 days in an airtight container.
To freeze: Flash freeze muffins on a sheet tray in the freezer for about 2 hours before placing them in an airtight container or Ziploc bag and freezing for up to 3 months.
To defrost: Thaw your frozen pumpkin cream cheese muffins overnight in the refrigerator and then either serve them chilled or bring them to room temperature prior to serving. 


Calories: 236kcal | Carbohydrates: 39g | Protein: 4g | Fat: 7g | Saturated Fat: 4g | Trans Fat: 1g | Cholesterol: 42mg | Sodium: 300mg | Potassium: 117mg | Fiber: 1g | Sugar: 23g | Vitamin A: 2985IU | Vitamin C: 1mg | Calcium: 59mg | Iron: 2mg