Step 1

Place racks in upper and lower thirds of oven; preheat to 350°. Toast pumpkin seeds on a large rimmed baking sheet on upper rack, tossing occasionally, until golden brown, 8–10 minutes. Let cool.

Step 2

Meanwhile, whisk flour, cocoa powder, kosher salt, baking soda, cinnamon, and paprika in a large bowl. Using an electric mixer on medium-high speed, beat brown sugar, granulated sugar, and butter in a large bowl until pale and fluffy, about 4 minutes. Add eggs one at a time, beating to blend after each addition. Reduce speed to low; add dry ingredients in 3 additions, mixing until well blended after each. Fold in chocolate and pumpkin seeds.

Step 3

Portion dough into 18 balls (about ¼ cup each) and divide between 2 parchment-lined baking sheets, spacing 3" apart. Sprinkle with sea salt and bake cookies, rotating pans halfway through, until edges are slightly browned and firm but centers are still soft, 18–20 minutes. Transfer to wire racks; let cool.