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Pumpkin Cream Cheese Muffins

Pumpkin cream cheese muffins topped with pumpkin seeds, with one muffin cut open to reveal a moist interior.

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These moist and spiced Pumpkin Cream Cheese Muffins are filled with a creamy cheesecake-style center and topped with optional pepitas. A cozy, homemade fall treat better than Starbucks and perfect for breakfast, snacks, or dessert.

Ingredients

Scale
  • 1½ cups (360ml) pure pumpkin puree
  • ½ cup (110g) packed light brown sugar
  • ½ cup + 2 tbsp (125g) granulated sugar
  • 2 large eggs, at room temperature
  • ½ cup (120ml) sunflower oil
  • 1 tsp pure vanilla extract
  • 2 cups (284g) all-purpose flour
  • 1½ tsp pumpkin pie spice
  • ½ tsp ground cinnamon
  • 1 tsp baking powder
  • ¾ tsp baking soda
  • ½ tsp salt
  • ⅓ cup (80ml) whole milk
  • 5 oz (142g) cream cheese, softened
  • 2½ tbsp (32g) granulated sugar (for filling)
  • 1 tsp all-purpose flour (for filling)
  • ½ tsp pure vanilla extract (for filling)
  • 2 tsp (10ml) whole milk (for filling)
  • Optional: chopped pumpkin seeds (pepitas) for topping

Instructions

  1. Preheat oven to 425°F and line a standard 12-cup muffin pan with liners.
  2. In a large bowl, whisk together pumpkin puree, brown sugar, granulated sugar, eggs, oil, and vanilla until smooth.
  3. In a separate bowl, combine flour, pumpkin pie spice, cinnamon, baking powder, baking soda, and salt.
  4. Fold the dry ingredients into the wet mixture. Midway, add milk and continue mixing until just combined. Let the batter rest for 30 minutes.
  5. In a small bowl, beat softened cream cheese, sugar, flour, and vanilla until smooth. Add milk and mix again. Transfer to a piping bag or zip-top bag.
  6. Divide the rested batter evenly among muffin cups, filling them to the rim.
  7. Pipe cream cheese filling into the center of each muffin (about ¼ inch deep) and swirl slightly on top if desired.
  8. Sprinkle pepitas around the cream cheese filling (optional).
  9. Bake at 425°F for 5 minutes, then reduce oven temperature to 350°F and bake an additional 12–15 minutes until a toothpick comes out clean.
  10. Let muffins cool in the pan for 5 minutes, then transfer to a wire rack to finish cooling.

Notes

  • Use canned pumpkin, not pumpkin pie filling.
  • Let batter rest for 30 minutes before baking for best texture.
  • Room temperature ingredients ensure smooth batter and filling.
  • Don’t overmix the batter to avoid dense muffins.
  • Muffins freeze well for up to 2 months—wrap individually for best results.

Nutrition