Preheat oven to 350°F. Line baking sheets with parchment paper. Set aside.
In a medium bowl, whisk together the flour, baking soda, and salt. Set aside.
In a large bowl, combine the melted butter, peanut butter, brown sugar, granulated sugar, eggs, and vanilla extract until smooth.
Gradually add the dry ingredients to the peanut butter mixture, mixing until fully combined.
Gently fold in most of the chocolate chips, peanut butter chips, and chopped mini Reese’s, reserving a few of each for topping the cookies.
Using a 2-tablespoon scoop, portion the dough onto the lined baking sheets, spacing each cookie about 2 inches apart.
Top each dough ball with a few of the reserved chocolate chips, peanut butter chips, and chopped peanut butter cups.
Bake for 13-15 minutes, or until the edges are golden brown. The centers may appear slightly underbaked but will set as they cool.
Let the cookies cool on the baking sheets for 5 minutes, then transfer them to a wire rack to cool completely.