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, cinnamon, nutmeg, and salt until well combined.
In another bowl, mix the granulated sugar, brown sugar, pumpkin puree, vegetable oil, eggs, and 1 teaspoon of vanilla extract until smooth.
Gradually add the dry ingredients to the wet ingredients, stirring until just combined. Be careful not to overmix.
In a separate bowl, beat the softened cream cheese, powdered sugar, and 1 teaspoon of vanilla extract until creamy and smooth.
Fill each muffin cup about halfway with the pumpkin batter. Add a spoonful of the cream cheese mixture on top of the batter, then cover with more pumpkin batter until the cups are about 3/4 full.
Bake in the preheated oven for 18-20 minutes, or until a toothpick inserted into 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.