Preheat oven to 375°F (190°C) and line a 12-cup muffin tin with paper liners.
In a medium bowl, whisk together the flour, baking soda, salt, cinnamon, ginger, cloves, and nutmeg.
In a large bowl, whisk the pumpkin puree, 0.5 cup granulated sugar, brown sugar, 2 eggs, vegetable oil, and 1 teaspoon vanilla extract until smooth.
Fold the dry ingredients into the wet ingredients using a spatula until just combined; do not overmix.
In a separate small bowl, beat the softened cream cheese, 0.25 cup granulated sugar, egg yolk, and remaining 0.5 teaspoon vanilla extract until creamy.
Distribute the pumpkin batter evenly among the 12 muffin cups.
Dollop approximately 1 tablespoon of the cream cheese mixture into the center of each muffin cup.
Use a toothpick to gently swirl the cream cheese into the pumpkin batter for a marbled effect.
Bake for 20 to 25 minutes, or until a toothpick inserted into the cake portion comes out clean.
Allow muffins to cool in the tin for 5 minutes before transferring to a wire rack to cool completely.