Preheat the oven to 350°F (175°C). Line a 12-cup muffin pan with paper liners or lightly grease it.

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

In a large bowl, whisk the pumpkin puree, granulated sugar, brown sugar, eggs, vegetable oil, milk, and vanilla until smooth.

Add the dry ingredients to the wet ingredients and stir just until combined. Do not overmix.

In a separate bowl, beat the softened cream cheese, maple syrup, powdered sugar, and vanilla until smooth and creamy.

Spoon about 1 tablespoon of pumpkin batter into each muffin cup. Add about 1 teaspoon of the maple cream cheese filling to the center of each, then cover with more batter until each cup is about 3/4 full.

Bake for 18 to 22 minutes, or until a toothpick inserted into the muffin portion comes out clean or with a few moist crumbs.

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