Preheat oven to 350°F (175°C). Line two baking sheets with parchment paper.
Brown the butter: Melt in a saucepan over medium heat for 5–8 minutes until golden and nutty. Stir in cocoa powder.
Melt chocolate: Add dark chocolate chips to the hot butter mixture and stir until smooth. Set aside to cool.
Whisk dry ingredients: Mix flour, baking powder, and salt in a bowl.
Mix wet ingredients: Beat eggs, granulated sugar, and brown sugar for 4–5 minutes until light and fluffy.
Combine: Fold in cooled chocolate mixture and vanilla. Gently incorporate dry ingredients.
Add chocolate chips: Fold in both types of chocolate chips. Chill dough 10–15 minutes if needed.
Scoop & bake: Form dough into balls, dip tops into extra chocolate chips, bake 11–12 minutes until crinkly.
Finish: Sprinkle with flaky sea salt. Let cool 5 minutes. Enjoy warm and gooey!