Preheat the oven to 350 F. Line two cookie sheets with parchment paper.
In a heatproof bowl, melt the butter in the microwave. Add the chocolate and stir until it has melted (if it doesn’t fully melt you can return it to the microwave for another 20-30 seconds).
Whisk in the sugar and peanut butter, then the salt, baking soda and vanilla. Whisk in the egg and egg yolk.
With a rubber spatula, stir in the cocoa and flour until you have a cohesive dough. Use a 2 tablespoon cookie scoop to portion the cookies onto the cookie sheets. Bake for 10 minutes.
When the cookies are out of the oven, leave them for about 3-5 minutes. Then, press a mini peanut butter cup into the center, just halfway down. Wait another 5 minutes or so, then gently press down again. Some of the pb filling will ooze out, that’s good! Once the pb cups are almost level with the cookie and the top of the cup is soft and melty, sprinkle on some sea salt. Serve warm or at room temperature, they’re absolutely delicious at any state.