Prep the basics: Line two baking sheets with parchment. Set butter and eggs out to warm slightly. Preheat the oven to 350°F (175°C) if baking right away.

Cream the fats and sugars: In a large bowl, beat the butter, peanut butter, granulated sugar, and brown sugar on medium speed for 2–3 minutes, until fluffy and lighter in color.

Add eggs and vanilla: Mix in the egg, then the extra yolk, followed by the vanilla. Beat until smooth and glossy, about 30 seconds.

Whisk dry ingredients: In a separate bowl, whisk the flour, baking soda, baking powder, and salt. This keeps leavening even and prevents clumps.

Combine gently: Add the dry ingredients to the wet mixture. Mix on low just until no dry streaks remain. Do not overmix—stop as soon as the dough comes together.

Fold in chocolate: Use a spatula to fold in the chocolate chunks, reserving a small handful for pressing on top before baking.

Chill (crucial): Cover and chill the dough for 30–60 minutes. This firms the dough, prevents spreading, and deepens flavor.

Portion the dough: Scoop into 2-tablespoon balls (about 40–45 g each). Space them at least 2 inches apart on the prepared sheets.

Top and bake: Press a few extra chocolate chunks into the tops. Bake for 9–11 minutes until edges are set and centers look slightly underbaked. Rotate sheets halfway through for even baking.

Finish and set: Immediately sprinkle with a pinch of flaky sea salt if you like. Let cookies cool on the sheet for 5 minutes, then transfer to a rack. They’ll firm up as they cool.