Heat oven to 350℉/177℃.
Line muffin tins with paper liners or spray with baking spray. Set aside.
In a small bowl, whisk together flour, baking powder, baking soda, and salt. Set aside.
In a microwave proof bowl, heat chocolate in 15 second increments, stirring after each, until chocolate is melted and smooth. Set aside.
With an electric mixer, beat butter and sugar until light and fluffy, about 2-3 minutes.
Beat in egg, egg yolk, and vanilla.
Mix in chocolate.
Add flour mixture alternately with milk, beginning and ending with flour mixture.
Use a 3 Tablespoon cookie scoop to portion batter into prepared pans.
Insert 1 peanut butter cup in center of each cupcake.
Cover peanut butter cup with ½ Tablespoon of batter.
Bake for 20-22 minutes, until puffed and cooked through.