Using a stand mixer, beat together the sugars and butter in a medium bowl until light and creamy. Add the egg, miso paste, and vanilla, and beat on medium until well mixed. Add flour and baking soda and beat just until combined. Use a spatula to fold in the chocolate chunks. Cover and refigerate for at least an hour (this will help the dough from spreading when baking).

Preheat oven to 350 degrees F (175 C). Spray two baking sheets with cooking spray or cover with parchment paper.

Use a medium ice cream scoop to portion the cookie dough onto the prepared baking sheets, leaving an inch or so between the cookies so they have room to spread.

Bake for 14 to 16 minutes (longer if you like your cookies crispier), rotating the trays halfway through, or until the cookies have browned all over.

Remove from oven, sprinkle with flaky sea salt, and let cool for 5 minutes before transfering to a wire rack to cool completely.