Prep Your Kitchen: Preheat oven to 350°F (175°C). Line two baking sheets with parchment paper.
Make the Cream Cheese Filling: In a medium bowl, beat together softened cream cheese, ¼ cup sugar, egg yolk, and vanilla until smooth and creamy. Set aside.
Mix Dry Ingredients: In a separate bowl, whisk together flour, baking soda, salt, cinnamon, nutmeg, ginger, and cloves.
Create Cookie Base: In a large mixing bowl, cream the softened butter with both sugars until light and fluffy (about 3 minutes). Beat in the egg, then add pumpkin puree and vanilla extract.
Combine: Gradually mix the flour mixture into the pumpkin mixture until just combined. Don't overmix.
Shape and Fill: Scoop 1½ tablespoons of cookie dough onto prepared baking sheets, spacing 2 inches apart. Make a small well in the center of each cookie and fill with 1 teaspoon of cream cheese mixture.
Bake: Bake for 12-14 minutes until edges are set but centers still look slightly soft.
Cool: Let cookies cool on baking sheet for 5 minutes before transferring to a wire rack.
