Step 1

Place racks in upper and lower thirds of oven; preheat to 350°. Mix cinnamon, ginger, nutmeg, and cloves in a small bowl to make pumpkin spice. Whisk flour, baking soda, salt, and 1 Tbsp. pumpkin spice in a medium bowl; set remaining pumpkin spice aside for making pies, quick breads, or another batch of cookies.

Step 2

Combine butter, brown sugar, and granulated sugar in the bowl of a stand mixer fitted with the paddle attachment. Beat on medium speed, scraping sides of bowl as needed until fluffy, about 3 minutes. Reduce speed to low and with motor running, add eggs one at a time, mixing to incorporate after each addition before adding the next. Beat in pumpkin purée and vanilla paste. Gradually add dry ingredients and beat just until combined (be careful not to overmix). Set aside a handful or so of each of the chopped chocolate, chocolate chips, and pecans. Using a rubber spatula, gently fold remaining chopped chocolate, chocolate chips, and pecans into dough.

Step 3

Using a No. 20 cookie scoop (about 3 Tbsp.), drop balls of dough onto two parchment-lined baking sheets, spacing at least 4" apart. (If using a half-sheet pan, bake 2 cookies per sheet. For a full sheet, you can fit about 4.) Gently press reserved chocolate and nuts into tops of dough balls.

Step 4

Bake cookies, rotating pans top to bottom and front to back halfway through, until golden brown around the edges, 11–13 minutes (subsequent batches may take 2–3 minutes longer). Let cookies cool on baking sheets 5 minutes.

Step 5

Using a thin metal spatula, carefully transfer cookies to wire racks and let cool completely.

Step 6

Do ahead: Dough can be made and formed into balls 3 months ahead; freeze on baking sheets until solid, then transfer to resealable freezer bags or an airtight container. Cookies can be baked 3 days ahead; store airtight at room temperature.