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

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

In a separate medium bowl, combine the pumpkin puree, eggs, vegetable oil, and vanilla extract until smooth.

Gradually add the wet ingredients to the dry ingredients and mix until just combined. Do not overmix.

In another bowl, prepare the cream cheese filling by beating together the softened cream cheese, 1/4 cup granulated sugar, and 1 teaspoon vanilla extract until smooth and creamy.

Fill each muffin cup about 2/3 full with the pumpkin batter.

Add a small dollop of the cream cheese mixture (about 1 teaspoon) on top of each muffin and gently swirl it into the batter using a toothpick or knife.

Bake the muffins in the preheated oven for 18-22 minutes, or until a toothpick inserted into the muffin (avoiding the cream cheese swirl) comes out clean.

Allow the muffins to cool in the tin for 5 minutes before transferring them to a wire rack to cool completely.