Prepare your oven and workspace. Preheat your oven to 350°F (175°C) and line two baking sheets with parchment paper. This prevents sticking and makes cleanup easier.
Mix the dry ingredients. In a medium bowl, whisk together flour, baking powder, baking soda, cinnamon, nutmeg, ginger, cloves, and salt until well combined. Set aside.
Cream the butter and sugars. In a large bowl using an electric mixer, beat the butter with both sugars until light and fluffy, about 2-3 minutes. Don’t rush this step—it creates the perfect texture base.
Add the wet ingredients to the butter mixture. Beat in the pumpkin puree, egg, and vanilla extract until well combined. The mixture might look slightly curdled, but that’s completely normal.
Combine wet and dry ingredients. Gradually add the flour mixture to the pumpkin mixture, mixing on low speed just until combined. Avoid overmixing to keep the cookies tender.
Prepare the cheesecake filling. In a separate bowl, beat the cream cheese, sugar, vanilla extract, and salt until smooth and creamy, about 2 minutes.
Shape the cookies. Using a medium cookie scoop (about 1½ tablespoons), scoop dough onto the prepared baking sheets, spacing them about 2 inches apart. Make a small indentation in the center of each cookie with your thumb or the back of a teaspoon.
Add the cheesecake filling. Fill each indentation with about 1 teaspoon of the cream cheese mixture. If using the optional topping, sprinkle the edges of each cookie with turbinado or cinnamon sugar.
Bake until perfect. Bake for 12-14 minutes or until the edges are set and just beginning to brown, while the centers remain soft. The cream cheese filling should be set but might still look slightly soft.
Cool completely before serving. Let the cookies cool on the baking sheets for 5 minutes, then transfer to a wire rack to cool completely. The filling will continue to set as they cool.