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

In a large mixing bowl, whisk together the flour, granulated sugar, brown sugar, baking soda, salt, cinnamon, nutmeg, ginger, and cloves.

In another bowl, combine the eggs, pumpkin puree, vegetable oil, and vanilla extract. Mix until smooth.

Gradually fold the wet ingredients into the dry ingredients, stirring until just combined. Do not overmix.

In a small bowl, prepare the cream cheese filling by mixing the softened cream cheese, 1/4 cup granulated sugar, egg yolk, and vanilla extract until smooth and creamy.

Fill each muffin liner about two-thirds full with the pumpkin batter.

Spoon a small dollop of the cream cheese filling onto the center of each muffin, then use a toothpick or skewer to gently swirl the cream cheese into the batter.

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

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