Preheat your oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners.

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

In a large mixing bowl, combine the pumpkin puree, granulated sugar, brown sugar, vegetable oil, eggs, and vanilla extract. Whisk until smooth.

Gradually add the dry ingredients to the wet ingredients and stir until just combined. Be careful not to overmix.

To make the cream cheese filling, in a small bowl, beat the softened cream cheese, granulated sugar, and vanilla extract until smooth and creamy.

Spoon a layer of pumpkin batter into each muffin cup, filling it about 1/3 of the way. Add a dollop (about 1 teaspoon) of the cream cheese mixture on top of the batter in each cup. Then, cover the cream cheese filling with more pumpkin batter until the cups are about 3/4 full.

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.

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