Preheat oven: 350°F. Line a muffin pan with muffin liners.
Mix dry ingredients: In a medium bowl, combine flour, baking powder, baking soda, salt, cinnamon, and nutmeg. Whisk to combine evenly.
Mix wet ingredients: In a separate large bowl, whisk together pumpkin puree, melted butter, eggs, vanilla extract, granulated sugar, and brown sugar until smooth.
Gradually add dry ingredients to the wet ingredients, mixing gently. Do not overmix.
Fill muffin pan: Scoop batter into the lined muffin pan, filling each about 2/3 full.
In a small bowl, beat together cream cheese and confectioner’s sugar until smooth. Transfer to a ziplock bag, cut off one corner, and pipe the filling into the center of each muffin.
Bake at 350°F for 20–25 minutes, or until a toothpick inserted near the edge comes out clean with some crumbs.
Let muffins cool slightly before serving.