Step 1
Place racks in upper and lower thirds of oven; preheat oven to 350°. Line two large rimmed baking sheets with parchment paper.
Step 2
Whisk 1 Tbsp. ground cinnamon, 1½ tsp. ground ginger, 1 tsp. ground nutmeg, and ¾ tsp. ground cloves in a small bowl to make pumpkin pie spice. Whisk 3 cups (375 g) all-purpose flour, 1¼ tsp. baking soda, 1 tsp. Diamond Crystal or ½ tsp. Morton kosher salt, and 1 Tbsp. pumpkin spice in a medium mixing bowl to combine. Set flour mixture aside; store remaining spice mix at room temperature, covered, up to 3 months to use in pies, quick breads, or another batch of cookies.
Step 3
Combine 1¼ cups (2½ sticks) unsalted butter, softened, 1½ cups (packed; 300 g) light brown sugar, and 1 cup (200 g) granulated sugar in the bowl of a stand mixer fitted with the paddle attachment (Alternatively, use a large bowl with a hand mixer or wooden spoon). Beat on medium speed, scraping sides of bowl as needed until fluffy, about 3 minutes. Reduce speed to low and, with motor running, add 3 large eggs, one at a time, mixing to incorporate after each addition before adding the next. Beat in ¼ cup pumpkin purée and 1 Tbsp. vanilla bean paste or extract. Gradually add dry ingredients to wet ingredients and beat just until combined (be careful not to overmix). Set aside a handful or so of each of 4 oz. (112 g) semisweet chocolate, coarsely chopped, 1½ cups (9 oz./255 g) dark chocolate chips, 1½ cups (174 g) coarsely chopped pecans. Using a rubber spatula, gently fold remaining chocolate and nuts into dough.
Step 4
Using a no. 20 cookie scoop (about 3 Tbsp.), drop balls of dough onto prepared baking sheets, spacing at least 4″ apart. (If using a quarter-sheet pan, bake 2 cookies per sheet. For a half-sheet, you can fit 4 or 5.) Gently press reserved chocolate and nuts into tops of dough balls.
Step 5
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 6
Using a thin metal spatula, carefully transfer cookies to wire racks and let cool completely.
Do Ahead: Cookie dough can be made and formed into balls 3 months ahead; freeze on cookie 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.
Editor’s note: This pumpkin chocolate chip cookie recipe was first printed in our November 2020 issue as ‘Pecan Pumpkin Spice Chocolate Chip Cookies.’ Head this way for move of our favorite cookies for Thanksgiving →