Preheat the oven to 350F. Line a 12-cup cupcake pan with paper liners and set aside.
In a small bowl, whisk together the cream cheese, sugar and vanilla until smooth.
½ cup cream cheese, softened, 2 tablespoons granulated sugar, ½ teaspoon pure vanilla extract
In a medium bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon, ginger, nutmeg and cloves.
1 ¾ cup all purpose flour, 1 ½ teaspoons baking powder, ½ teaspoon baking soda, ¾ teaspoon fine sea salt, 1 teaspoon ground cinnamon, ½ teaspoon ground ginger, ¼ teaspoon ground nutmeg, ⅛ teaspoon ground cloves
In a large bowl, whisk together the granulated sugar, brown sugar, pumpkin, vanilla, eggs and oil.
¾ cup granulated sugar, ½ cup brown sugar, packed, 1 ¼ cup pumpkin puree, 1 teaspoon pure vanilla extract, 2 large eggs, ½ cup canola oil
Pour the dry ingredients into the wet ingredients and mix to combine. Do not over mix. Only mix until no pockets of the dry ingredients remain.
Divide the batter equally into the lined cupcake pan.
Distribute the cream cheese filling into the centers, equally among the muffins.
Mix together the 1 tablespoon of sugar and the ½ teaspoon of cinnamon in a small bowl. Sprinkle the pepitas and the cinnamon sugar mixture around the edge of the muffins.
1 tablespoon granulated sugar, ½ teaspoon ground cinnamon, 2 tablespoons pepitas
Bake the muffins for 18-22 minutes or until a toothpick inserted comes out with a few dry crumbs. Do not check the muffins for doneness by inserting a toothpick through the cream cheese center. Check by inserting a toothpick through the muffin at an angle.
Cool the muffins in the pans for 10 minutes before removing to cool on a cooling rack. Best served slightly warm.