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

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

In a large bowl, whisk the eggs, granulated sugar, brown sugar, pumpkin puree, vegetable oil, 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 cream cheese, sugar, egg yolk, and vanilla until smooth and creamy.

Divide the pumpkin muffin batter evenly among the prepared muffin cups, filling each about 3/4 full.

Spoon about 1 tablespoon of the cream cheese mixture onto the top of each muffin. Use a toothpick or knife to gently swirl it into the batter, if desired.

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

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