Preheat your oven to 375°F (190°C) and line a 12-cup muffin tin with paper liners or grease the cups.

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

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

Gradually add the dry ingredients to the wet ingredients, mixing gently until just combined. Be careful not to overmix.

In a separate small bowl, beat the softened cream cheese, granulated sugar, egg yolk, and vanilla extract until smooth and creamy.

Fill each muffin cup about 2/3 full with the pumpkin batter. Add a small dollop (about 1 teaspoon) of the cream cheese mixture to the center of each muffin cup.

Using a toothpick or skewer, gently swirl the cream cheese mixture into the pumpkin batter to create a marbled effect.

Bake the muffins in the preheated oven for 18-22 minutes, or until a toothpick inserted into the center of a muffin comes out clean.

Remove the muffins from the oven and let them cool in the muffin tin for 5-10 minutes before transferring them to a wire rack to cool completely.