Start by preheating your oven to 350°F (175°C). This ensures that your cookies will bake evenly.
In a medium bowl, whisk together the flour, baking soda, and salt. Set this mixture aside.
In a large mixing bowl, cream together the softened butter, peanut butter, brown sugar, and granulated sugar until light and fluffy.
Beat in the egg and egg yolk, along with the vanilla extract, until well combined.
Gradually add the dry ingredient mixture to the wet ingredients, mixing on low speed until just combined.
Gently fold in the mini semisweet chocolate chips using a spatula or wooden spoon.
Using a cookie scoop, portion out about 1 tablespoon of dough, flatten it in your hand, place a peanut butter cup in the center, and wrap the dough around it.
Line your baking sheets with parchment paper and place the stuffed cookie dough balls on the sheets, leaving space between each one.
Bake in the preheated oven for 10-12 minutes, or until the edges are lightly golden.
Once baked, let the cookies cool on the baking sheets for about 5 minutes before transferring them to a wire rack to cool completely.