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

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

In another bowl, mix the granulated sugar, brown sugar, pumpkin puree, vegetable oil, eggs, and vanilla extract until well combined.

Pour the wet ingredients into the dry ingredients and gently fold them together until just combined; avoid over-mixing.

In a separate bowl, beat the softened cream cheese, powdered sugar, and vanilla extract together until smooth.

Spoon about 2 tablespoons of the muffin batter into each muffin cup. Add a dollop of the cream cheese mixture on top, then add a little more muffin batter, creating a layer effect.

Using a toothpick or a knife, gently swirl the cream cheese filling into the muffin batter.

Place the muffin tin in the preheated oven and bake for 18-22 minutes, or until a toothpick inserted in the center comes out clean.

Allow the muffins to cool in the pan for 5 minutes before transferring them to a wire rack to cool completely.