Preheat your oven to 375°F (190°C). Line a muffin tin with paper liners or lightly grease the cups.

In a medium bowl, whisk together the flour, baking soda, baking powder, salt, cinnamon, nutmeg, and ginger. Set aside.

In a large mixing bowl, combine the pumpkin puree, granulated sugar, brown sugar, 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. Be careful not to overmix.

In a separate bowl, prepare the cheesecake filling by beating together the softened cream cheese, 1/4 cup granulated sugar, and 1 teaspoon vanilla extract until smooth and creamy.

Spoon about 1 tablespoon of the pumpkin batter into the bottom of each muffin cup. Add a teaspoon of the cheesecake filling on top, then cover with another tablespoon of pumpkin batter until the cups are about 2/3 full.

Bake in the preheated oven for 18-22 minutes, or until a toothpick inserted into the muffin (avoiding the cheesecake center) comes out clean.

Allow the muffins to cool in the pan for 5 minutes, then transfer them to a wire rack to cool completely.