Heat oven to 350℉/177℃.
Line 2 sheet pans with parchment paper. Set aside.
In a small bowl, whisk together flour, baking powder, baking soda, and salt. Set aside.
With an electric mixer, beat butter, peanut butter, and sugars until light and fluffy, about 2-3 minutes.
Add egg, egg yolk, and vanilla.
Beat until fully incorporated.
Add flour mixture.
Stir until combined.
Using a 3 Tablespoon cookie scoop, portion dough.
Working with 1 scoop of dough at a time, flatten, place peanut butter cup in center, and fold dough around it.
Place on prepared pan.
Bake for 16-18 minutes, or until cookie is completely set.
Allow to cool on pans.