Preheat oven to 350°F and set aside a greased muffin tin (or line with cupcake liners).
In a small bowl, whisk together cream cheese filling ingredients until smooth. Transfer to a piping bag and set aside.
In a medium bowl, whisk together all-purpose flour, cinnamon, cloves, cardamom, ginger, nutmeg, baking powder, baking soda, and salt. Set aside.
In a large bowl, whisk pumpkin puree, eggs, oil, brown sugar, granulated sugar, and vanilla until smooth. Gently add prepared flour mixture, and fold until no lumps remain.
Transfer the batter to the prepared cupcake pan, filling to the rim. Pipe the cream cheese mixture into each muffin (the piping bag only needs to be inserted about ¼-inch deep), pulling up slowly so that the filling pours out the top and is visible on the surface of the muffin. Top each muffin with pepitas, if using.
Bake until an inserted toothpick near the center comes out clean, about 15 to 20 minutes. Cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.