Preheat your oven to 350°F (175°C) and line a muffin pan with paper liners.

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

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

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

In a small bowl, beat together the softened cream cheese, powdered sugar, and vanilla extract until smooth and creamy.

Fill each muffin liner about 3/4 full with the pumpkin batter.

Spoon about 1 teaspoon of the cream cheese mixture into the center of each muffin, gently pushing it into the batter.

Sprinkle a few pepitas (pumpkin seeds) on the top of each muffin for texture and decoration.

Bake in the preheated oven for 18-22 minutes, or until a toothpick inserted near the edge of a muffin comes out clean (avoid testing through the cream cheese center).

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