Preheat oven to 350‡F and line a baking sheet with parchment paper. Set aside.
In a medium bowl, whisk together all-purpose flour, cocoa powder, sea salt, baking soda, and baking powder. Set aside.
Add sugars and butter to your stand mixer and cream together for about 3 minutes, scraping down the sides if necessary.
Add egg, egg yolk and pure vanilla extract and mix until just combined.
Mix flour mixture in the wet ingredients until combined, then run to combine peanut butter chips and peanut butter cups.
Using a 3-tablespoon cookie scoop, scoop balls.
If desired, add extra peanut butter cups to the tops of the cookie dough and bake for 9 minutes or until lightly golden.
Allow to cool on the baking sheet for 5-10 minutes, then transfer to a wire rack.