Make the Cheesecake Filling: Beat the softened cream cheese, granulated sugar, vanilla extract, sour cream, and flour until smooth and creamy. Scoop the mixture into small portions onto a parchment-lined baking sheet and freeze until firm.
Prepare the Pumpkin Puree: Spread the pumpkin puree over paper towels and gently blot away excess moisture. This helps prevent the cookie dough from becoming too wet.
Mix the Dry Ingredients: Whisk together the flour, pumpkin pie spice, baking powder, baking soda, and salt in a medium bowl.
Cream the Butter and Sugars: Beat the softened butter, brown sugar, and granulated sugar until light and fluffy. Add the egg yolks and mix until combined.
Add the Pumpkin: Mix the prepared pumpkin puree into the butter mixture until smooth and evenly combined.
Make the Pumpkin Spice Sugar: Combine the granulated sugar and pumpkin pie spice in a small bowl. Set aside for coating the cookies.
Stuff the Cookies: Take a portion of chilled cookie dough and flatten it gently. Place a frozen cheesecake filling portion in the center, then carefully wrap the dough around it and seal completely.
Coat the Cookies: Roll each stuffed cookie dough ball in the pumpkin spice sugar until evenly coated.
Chill Before Baking: Arrange the coated cookie dough balls on a parchment-lined baking sheet and chill until firm.
Bake the Cookies: Preheat the oven to 350°F (175°C). Bake the cookies until the edges are set and lightly golden, about 11–13 minutes. Do not overbake.
Cool and Serve: Let the cookies cool on the baking sheet for several minutes, then transfer them to a wire rack. Cool before serving to allow the cheesecake center to set.