In a medium bowl, whisk the flour, baking powder, salt, cinnamon, and nutmeg together. Set aside.
In a kitchenaid mixer with a paddle attachment, beat together the butter and sugars on medium high speed until fluffy about 2-3 minutes.
Blend in pumpkin puree, beat in egg and then add vanilla. Slowly add dry ingredients on low speed just until combined. Cover and chill dough for an hour.
To make the cream cheese filling, blend cream cheese, sugar and vanilla together. Chill for an hour.
Preheat oven to 350 and line your baking sheets with parchment paper. In a small bowl, combine the sugar and spices for the coating and set aside.
To make the cookies, take a tablespoon of the cookie batter. Flatten it like a pancake and place a teaspoon of the cream cheese in center. Form another tablespoon of the cookie batter into a flat pancake shape and place on top of the cream cheese. Pinch the edges together sealing in the cream cheese and roll into a ball. Roll in the cinnamon sugar coating and place on the prepared baking sheet 2 inches apart.
Repeat until the dough is gone and flatten the cookie dough balls with a heavy bottomed glass or measuring cup.
Bake the cookies for 10-15 minutes or until the tops start to crack. Let cool on the baking sheet for 5 minutes and transfer to a wire rack. Enjoy!