Line an 9-inch square baking pan with parchment paper. Set aside.
In a large bowl, combine the melted butter, gluten-free graham cracker crumbs, and confectioners' sugar until combined. Mix in 1 cup of peanut butter. Spread evenly into prepared baking pan.
Melt chocolate chips and remaining 2 Tablespoons of peanut butter in a double boiler, stirring until smooth. Spread over peanut butter layer.
Refrigerate for two hours. Allow to sit for 15 minutes before cutting into squares.