Preheat the oven to 350°F. Line two baking sheets with parchment paper and set aside. Whisk together the flour, cocoa powder, baking soda, and salt. Set aside.
in microwave-safe mixing bowl, melt the butter. Add the white and brown sugars and mix until well combined and the sugars begin to dissolve (a hand mixer works well here).
Add the egg, egg yolk, and vanilla. Continue to mix until sugar nearly dissolves.
Add in the dry ingredients and stir to combine.
Fold in the chocolate chips until combined.
Weigh out the dough into 100g portions and roll each into a ball. The balls will be slightly large than a golf ball. There will be about 9 equal portions.
Place the rolled cookie dough on the prepared baking pans, at least three inches apart. Slightly flatten each cookie and bake for 13 to 14 minutes. When done, the edges should be set but the centers will remain soft. Repeat with the remaining dough. Cool the cookies on the baking sheet over a wire cooling rack. Sprinkle with flaky salt, if desired.
Cool the cookies on the baking sheet for about 5 minutes then carefully transfer them to a wire cooling rack. Sprinkle with flaky salt, if desired.