Prepare the Cream Cheese Filling:
In a mixing bowl, beat the cream cheese, powdered sugar, and vanilla extract until smooth. Transfer the mixture to a piping bag or cover and refrigerate until ready to use.
Preheat the Oven:
Preheat your oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners.
Mix the Dry Ingredients:
In a medium bowl, whisk together the flour, baking soda, baking powder, salt, cinnamon, nutmeg, and ginger.
Mix the Wet Ingredients:
In a large bowl, combine the pumpkin puree, granulated sugar, brown sugar, oil, eggs, and vanilla extract. Mix until smooth.
Combine Wet and Dry Ingredients:
Gradually add the dry ingredients to the wet ingredients, mixing until just combined. Do not overmix.
Assemble the Muffins:
Fill each muffin liner about ⅔ full with pumpkin batter. Pipe or spoon a dollop (about 1 tbsp) of the cream cheese filling into the center of each muffin. Optionally, sprinkle the tops with a cinnamon-sugar mixture.
Bake:
Bake in the preheated oven for 18–22 minutes, or until a toothpick inserted into the muffin (avoiding the cream cheese center) comes out clean.
Cool and Serve:
Let the muffins cool in the tin for 5 minutes, then transfer them to a wire rack to cool completely. Serve warm or at room temperature.