Prepare Your Ingredients - Begin by gathering all your ingredients to ensure a smooth baking process. Allow the butter to soften at room temperature for about 30 minutes before starting. This will help it cream properly with the sugars. Set out the eggs to bring them closer to room temperature as well, which helps them incorporate better into the dough.
Mix the Dough - In a stand mixer fitted with the paddle attachment, cream together the softened butter, brown sugar, and granulated sugar on medium speed for 2 minutes until light and fluffy. Add the eggs one at a time, followed by the vanilla extract, mixing until the batter is smooth and well combined. Gradually add the flour, mixing on low speed until just incorporated to avoid overmixing. Using a spatula, gently fold in the chocolate chips until evenly distributed throughout the dough.
Chill the Dough - Cover the cookie dough with plastic wrap and refrigerate for 30-48 hours. While this step is optional, it allows the flavors to develop fully and results in a richer, more flavorful cookie. The chilled dough will also hold its shape better during baking.
Preheat and Prepare - Preheat your oven to 375°F (190°C) and lightly grease a 24-cup mini muffin tin. If you don't have a mini muffin tin, you can use a regular one but adjust the amount of dough used accordingly.
Form and Bake - Scoop the chilled dough and roll into balls about 1-1.5 inches in diameter. Place each ball into the cups of the mini muffin tin. Bake for 8-10 minutes until the edges are just beginning to turn golden brown. The centers should still be slightly soft.
Add Reese's Cups - Remove the muffin tin from the oven and immediately press a Reese's miniature into the center of each cookie cup, pushing down so the top of the candy is level with the cookie. Return to the oven and bake for an additional 1-2 minutes to allow the chocolate to soften slightly.
Cool and Serve - Allow the cookie bites to cool in the muffin tin for 10-15 minutes. Then, carefully remove them and transfer to a wire rack to cool completely. The peanut butter cups will be very soft at first but will firm up as they cool.