Prepare the Cream Cheese Filling: Beat the softened cream cheese, powdered sugar, vanilla extract, and flour until smooth and creamy. Refrigerate the filling while preparing the pumpkin batter.
Prepare the Oven and Pan: Preheat the oven to 375°F (190°C). Line a 12-cup muffin pan with paper liners.
Mix the Dry Ingredients: In a medium bowl, whisk together the flour, baking soda, baking powder, salt, cinnamon, ginger, nutmeg, and cloves until evenly combined.
Mix the Wet Ingredients: In a large bowl, whisk together the pumpkin purée, granulated sugar, brown sugar, eggs, vegetable oil, and vanilla extract until smooth.
Combine the Batter: Gradually add the dry ingredients to the pumpkin mixture. Stir gently with a spatula just until combined. Do not overmix.
Fill the Muffin Cups: Add a layer of pumpkin batter to each muffin liner. Add a spoonful of the chilled cream cheese filling to the center, then cover with more pumpkin batter.
Add Optional Toppings: Sprinkle the tops with pepitas and a light dusting of cinnamon if desired.
Bake: Bake for 20–24 minutes, or until the pumpkin portion is set and a toothpick inserted into the muffin portion comes out mostly clean.
Cool: Let the muffins cool in the pan for about 10 minutes, then transfer them to a wire rack to cool completely.
Serve: Serve at room temperature or slightly warm with coffee, tea, or your favorite fall beverage.