Preheat your oven to 325°F (163°C). This ensures that your cheesecakes bake evenly.
Line a mini muffin tin with parchment paper or mini cupcake liners.
In a medium bowl, combine graham cracker crumbs, sugar, and melted unsalted butter. Mix until well coated.
Scoop about 1 tablespoon of the crust mixture into each muffin cup, pressing down firmly. Bake for 5 minutes and then remove from the oven to cool slightly.
In a large mixing bowl, beat cream cheese until smooth. Gradually add sugar and mix well. Then add flour, eggs, and vanilla. Mix until smooth.
Fold in Reese's Peanut Butter chips into the cheesecake mixture.
Place a miniature Reese's Peanut Butter Cup at the bottom of each muffin cup. Pour the cheesecake batter over the top, filling each cup about ¾ full.
Bake in the preheated oven for 18-20 minutes, until the centers are set but still slightly jiggly.
Allow cheesecakes to cool in the pan for 10 minutes, then transfer to a wire rack to cool completely. Refrigerate for at least 2 hours.
In a microwave-safe bowl, combine chocolate chips and shortening. Microwave until melted and smooth. Drizzle over the cooled cheesecakes before serving.
