Preheat the oven to 375°F (190°C) and line a muffin tin with paper liners.

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

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

Gradually mix the wet ingredients into the dry ingredients until just combined. Be careful not to overmix.

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

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

Spoon a small dollop (around 1 teaspoon) of the cream cheese mixture onto the center of each muffin and lightly press it down into the batter.

Sprinkle pepitas (pumpkin seeds) over the tops of the muffins for added texture and flavor.

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

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