Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners or grease it well.
In a large bowl, whisk together the flour, sugar, baking soda, baking powder, salt, cinnamon, and nutmeg until well combined.
In a separate bowl, mix the pumpkin puree, eggs, and oil until smooth and creamy.
Gradually add the wet mixture to the dry mixture, folding gently until just combined—be careful not to overmix!
In another bowl, whisk the cream cheese until smooth. You can sweeten it slightly with sugar or vanilla extract if desired.
Spoon half of the pumpkin batter into each muffin liner. Add about a tablespoon of cream cheese mixture in the center, then top with the remaining pumpkin batter.
Place the muffin tray in the oven and bake for 18-22 minutes, or until a toothpick comes out clean from the pumpkin portion.
Allow the muffins to cool in the tray for about 5 minutes before transferring them to a wire rack to cool completely.