Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease lightly.

In a large bowl, whisk together the flour, granulated sugar, brown sugar, baking soda, baking powder, salt, pumpkin pie spice, and cinnamon.

In a separate bowl, whisk the eggs, pumpkin puree, vegetable oil, milk, and vanilla extract until smooth.

Add the wet ingredients to the dry ingredients and stir just until combined. Do not overmix.

In a small bowl, beat the cream cheese, sugar, flour, and vanilla extract until smooth and creamy.

Divide half of the pumpkin batter evenly among the muffin cups.

Add about 1 teaspoon of the cream cheese mixture to the center of each muffin cup, then top with the remaining pumpkin batter.

Use a toothpick or skewer to gently swirl the cream cheese filling into the top of the batter if desired.

Sprinkle the tops with pepitas, if using.

Bake for 18 to 22 minutes, or until a toothpick inserted into the muffin portion comes out clean or with just a few moist crumbs.

Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.