Preheat your oven to 350°F (175°C) and prepare a muffin tin.
In a large mixing bowl, whisk together the dry ingredients: flour, baking soda, baking powder, cinnamon, nutmeg, and salt.
In a separate bowl, combine the sugar, oil, pumpkin puree, eggs, and vanilla extract. Mix until smooth.
Gradually add the dry ingredients to the wet mixture, stirring until just combined. Don't overmix.
In a smaller bowl, mix together cream cheese and powdered sugar until smooth and creamy.
Fill each muffin cup halfway with the pumpkin batter, then add a dollop of the cream cheese mixture, followed by more batter to fill the cups about 3/4 full.
Bake in the preheated oven for 18-20 minutes, or until a toothpick inserted in the center comes out clean.
Remove from the oven and allow the muffins to cool in the pan for 5 minutes before transferring to a wire rack.
Enjoy your fresh-baked pumpkin cream cheese muffins warm or at room temperature.