Whisk together your flour, baking soda, and baking powder in a medium bowl. Set aside.
In a small saucepan over medium-low heat, melt the butter. Once melted, increase the heat to medium and let the butter begin to foam. Keep cooking and stirring with a spatula, until the butter begins to brown and gives off a nutty smell (2-3 minutes). Pour into a medium bowl and let cool completely.
Add in the sugars, miso paste, vanilla and salt to the butter mixture. Whisk to combine.
Add in the egg and egg yolk and whisk until smooth and glossy.
Pour in the dry ingredients and use a rubber spatula to combine until there are no more streaks of flour.
Add in your chopped chocolate, but keep about ¼ cup of chopped chocolate to the side.
Scoop out the cookie dough using a 2 tablespoon ice cream scooper and place on a lined tray. Once finished, gently press the extra chocolate on top of the cookie dough balls - this will give you those puddles of chocolate! Chill for at least 30 minutes or up to overnight.
Preheat your oven to 350°F/175°C and line 3 baking trays with parchment paper.
Bake the cookies 6 at a time for 10-12 minutes.
Notes
Chocolate Chips: If you prefer using chips, sub out the same weight of chocolate for bittersweet or semisweet chocolate chips. I also enjoy doing 4 oz semisweet chips and 4 oz bittersweet chips. Miso Paste: you will want to use white miso paste here. Feel free to decrease it to just 1 tablespoon if you prefer! Salt: I'm using kosher salt, but if you only have fine salt then half the amounts listed (1 teaspoon kosher salt = ½ teaspoon fine salt). Please note, I'm using Diamond Crystal Kosher Salt and not Morton Salt. Morton salt is much saltier! Butter: I use European style butter in my recipes. StorageKeep the cookies in an airtight container for up to 5 daysFreezing InstructionsOnce you've reached step 8 and have chilled the cookie dough for 30 minutes, place the chilled cookie dough into a freezer bag. Keep in your freezer for up to 2 months. When ready to use, follow the baking instructions in the recipe and add a couple more minutes to the baking time.