Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners or grease it lightly.
In a large bowl, whisk together the flour, baking soda, baking powder, cinnamon, nutmeg, and salt. Set aside.
In another bowl, combine the granulated sugar, brown sugar, pumpkin puree, vegetable oil, eggs, and vanilla extract. Mix until smooth and well combined.
Gradually add the dry ingredients to the wet ingredients, stirring until just combined. Do not overmix.
In a small bowl, beat the softened cream cheese with the powdered sugar until 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 18-22 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.