Line your 9x9 inch pan with parchment paper, leaving overhang on the sides for easy removal.
Combine the peanut butter, butter, and vanilla extract in a microwave-safe bowl. Microwave in 30-second bursts, stirring after each, until the mixture is smooth and glossy.
Gradually add the powdered sugar to the peanut butter mixture, stirring well after each addition until the mixture is thick, smooth, and easy to spread.
Press the peanut butter mixture evenly into the prepared pan, using a spatula to smooth the surface. Chill in the refrigerator for about 30 minutes until firm.
While the base chills, melt the chocolate chips in a microwave-safe bowl. Microwave at 50% power in 20-second intervals, stirring each time until the chocolate is smooth and shiny.
Remove the peanut butter layer from the refrigerator and pour the melted chocolate over it, spreading evenly with a spatula to cover completely.
Sprinkle optional crushed nuts or sea salt flakes on top for added texture and flavor, then return the pan to the fridge. Chill for at least 2 hours until the chocolate is set and firm.
Use the parchment overhang to lift the bars out of the pan. Place on a cutting board and slice into 12 even bars with a sharp knife.
Serve immediately or store in an airtight container in the fridge for up to a week. For longer storage, freeze the bars and thaw before serving.