Preheat oven to 350°F. Spray a muffin tin with cooking spray.
In a small saucepan, heat the chocolate, peanut butter and butter over low heat, stirring constantly. Once melted, remove from heat and let cool 5 minutes.
In a large mixing bowl, add sugar, eggs and vanilla extract. Beat on high speed for 2 to 3 minutes. Pour in chocolate and beat on low speed until combined. Beat in flour on low speed until combined.
Add a tablespoon of brownie batter to each muffin tin. Place a Reese’s Peanut Butter Cup on top of each. Slightly press down to embed the peanut butter cup in the batter. Add about a teaspoon of brownie batter on top of each and spread to cover. Your peanut butter cup will now be fully encased inside the brownie.
Bake for 20 minutes. Let cool in the pan before removing onto a cooling rack.