In a medium-sized bowl, whisk the flour, pumpkin pie spice, baking powder, baking soda, and salt together. Set aside.
Add the butter and sugars to the bowl of a stand mixer. Cream them together until the mixture is light and fluffy. Scrape down the sides of the bowl as needed.
Add the egg and vanilla extract, mixing until well combined.
A little bit at a time, add the dry ingredients to the wet. Mix between additions. Scrape down the sides of the bowl as needed.
Add the chocolate chips and mix until they are distributed throughout the dough.
Using a 1 tablespoon cookie scoop, scoop the dough onto a baking sheet lined with parchment paper. Chill the dough in the fridge for at least an hour (and up to overnight). This will help to prevent the dough from spreading excessively.
Once you're ready to bake the cookies, preheat your oven to 350 degrees F. Line a couple of baking sheets with parchment paper. Place the chilled balls of dough on the prepared baking sheets. You will need to do this in batches. I baked 9 cookies per baking sheet.
Bake the cookies for 13-15 minutes, or until the edges are just turning golden.
Remove them from the oven and immediately press the chopped dark chocolate into the tops of the cookies.
Allow the cookies to cool on the baking sheets for 5 minutes before removing them to a wire rack to finish cooling.