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

In a medium bowl, whisk together the flour, baking soda, baking powder, cinnamon, nutmeg, ginger, and salt.

In a large bowl, whisk the pumpkin puree, granulated sugar, brown sugar, eggs, vegetable oil, and 1 teaspoon vanilla until smooth.

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

In a separate small bowl, beat the cream cheese, powdered sugar, milk, and 1/2 teaspoon vanilla until smooth and creamy.

Divide half of the pumpkin batter evenly among the muffin cups. Spoon about 1 tablespoon of the cream cheese mixture into the center of each muffin cup, then cover with the remaining pumpkin batter.

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

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

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