Start by browning your butter. Add the full cup of unsalted butter to a light colored saucepan over medium low heat. Let it melt completely, then keep swirling the pan as it foams and bubbles. After about 6 to 8 minutes the milk solids at the bottom will turn a deep golden brown and it will smell like toasted nuts. Pull it off the heat right away and pour everything, browned bits included, into a large mixing bowl.
Let the brown butter cool for a full 5 minutes before you do anything else. This matters! If it is too hot when it hits the eggs later it will start to scramble them, and we are not doing that.
Whisk the light brown sugar and granulated sugar into the cooled brown butter until everything is glossy and combined. It will look a little grainy and that is exactly right.
Add the eggs, vanilla extract, and pumpkin puree. Whisk until the mixture is completely smooth and uniform. It should look silky and pale orange.
In a separate bowl, whisk together the all purpose flour, pumpkin pie spice, cinnamon, baking powder, and salt. Getting the leavening and spices evenly distributed now means no surprise pockets later.
Fold the dry ingredients into the wet ingredients with a spatula until JUST combined. A few streaks of flour are fine at this point. Overmixing is what turns cookies tough, so go gently.
Now chop your chocolate. Take your dark chocolate bar and coarsely chop it on a cutting board, leaving some big chunks and some little shards. Fold it in along with the semi sweet chocolate chips until everything is evenly scattered through the dough.
Cover the bowl and refrigerate for 30 minutes. Please do not skip this! The pumpkin adds a lot of moisture and the chill is what keeps these thick and chewy instead of flat.
Preheat your oven to 350 degrees F and line your baking sheets with parchment paper. Scoop the chilled dough into balls, about 2 tablespoons each, and space them a couple of inches apart.
Bake for 10 to 12 minutes, until the edges are set and the centers still look slightly underdone and puffy. They will look a little soft in the middle and that is EXACTLY what you want. Pull them now.
Let them cool completely on the pan. This is the step everyone rushes and it is the whole secret to the chewy texture. They finish setting up as they cool, so give them time.
Finish with a pinch of flaky sea salt on top if you would like, then get ready for these to disappear immediately!