Preheat your oven to 350°F (175°C) and line a cookie sheet with parchment paper to keep your cookies from sticking and make cleanup simple.
In a large bowl, beat together the softened butter, cream cheese, light brown sugar, and granulated sugar until the mixture is creamy, fluffy, and light. Scrape the sides a couple of times so everything is evenly combined, this will give your cookies a tender, rich base.
Add the egg yolk and vanilla, stirring until they’re completely absorbed into the batter. The dough should feel soft, smooth, and lightly fragrant.
In a separate bowl, whisk together the flour, cinnamon, and ginger until evenly blended. Gradually fold this spiced flour mixture into the dough in two batches, using a spatula to combine gently. The dough will be thick and slightly sticky, that’s exactly what we want.
Scoop the dough into balls using a medium cookie scoop or about 2 tablespoons of dough each. Place them about 2 inches apart on the prepared cookie sheet so they have room to spread slightly.
Whisk together the pumpkin puree, egg, light brown sugar, milk, cinnamon, and ginger in a separate bowl until smooth.
Using a spoon, press a shallow well into the center of each cookie and fill it with the pumpkin mixture. Don’t worry about making it perfect.
Bake the cookies for 13–16 minutes, until the edges are lightly golden and the bottoms are set. The centers might still look a little soft, but they’ll firm up as they cool.
Move the cookies onto a cooling rack and let them rest until they’ve cooled all the way through. This step helps the pumpkin filling set while keeping the cookies tender. Enjoy!