Preheat the oven to 350ºF (≈175ºC). Line baking sheets with parchment paper.

In the bowl of an electric mixer, beat the butter, granulated sugar, and brown sugar until creamy, about 3 minutes. Scrape down the sides and bottom of the bowl. Add the vanilla and eggs and beat until combined, scraping as needed.

In a separate bowl, whisk together the dry ingredients for the chocolate‑chip dough (flour, baking soda, salt). Add half of the creamed butter‑sugar‑egg mixture (should weigh about 330 g if measured) into the flour mix, stirring with a rubber spatula into a cohesive dough. Mix in the chocolate wafers, reserving some for garnish.

To the remaining butter‑sugar mixture, add the flour for the cocoa dough, cocoa powder, baking soda and salt. Beat on low speed just until combined. Mix in the chocolate wafers, reserving some for garnish.

Using a medium 1½‑tablespoon cookie scoop, portion out dough from both doughs. For each cookie ball: tear one ball of the classic chocolate‑chip dough in half and sandwich the cocoa dough ball in between (or vice versa). Roll between your palms into a smooth ball. Place on the prepared baking sheet. Dot the top with additional chocolate wafers/chips for garnish. Repeat with all dough balls.

If you have time, wrap the shaped dough balls tightly in plastic wrap and refrigerate for at least 24 hours (and up to 72 hours). This “marinating” period helps produce thicker, chewier cookies with better flavor.

Bake for 11‑13 minutes, or until golden brown at the edges. Immediately after removing from oven, sprinkle with flaky sea salt if desired. Allow the cookies to rest on the baking sheet for 5 minutes before transferring them to a wire rack to cool completely.