Toast the pecans. Heat the oven to 350°F (175°C). Spread pecans on a baking sheet and toast for 6–8 minutes, until fragrant. Cool completely and roughly chop.

Whisk dry ingredients. In a medium bowl, whisk flour, baking soda, baking powder, and fine sea salt. Set aside.

Cream butter, miso, and sugars. In a large bowl, beat the softened butter, miso paste, granulated sugar, and brown sugar until light and fluffy, about 2–3 minutes. This builds structure and dissolves some sugar for better chew.

Add eggs and vanilla. Beat in the egg, then the egg yolk, followed by the vanilla. Mix until smooth and glossy.

Combine wet and dry. Add the dry ingredients and mix on low just until the flour disappears. Do not overmix.

Fold in the good stuff. Stir in chocolate and toasted pecans with a spatula. The dough will be thick and slightly tacky.

Chill (optional but helpful). Chill the dough for 30–60 minutes for thicker cookies and deeper flavor. If you’re in a rush, you can bake right away; they’ll spread a bit more.

Portion and bake. Line a baking sheet with parchment. Scoop 2-tablespoon mounds (about golf-ball size), spacing 2 inches apart. Bake at 350°F (175°C) for 10–12 minutes, until edges are set and centers look slightly underdone.

Finish and cool. Sprinkle with flaky sea salt while hot, if using. Let cookies cool on the sheet for 5 minutes, then move to a rack to finish setting.