Preheat the oven to 350°F. Line a 9 x 9-inch baking dish with parchment paper, leaving a 1-inch overhang on two sides.
In a large microwave-safe bowl, combine the butter and 1.5 cups of the chocolate chips. Microwave in 30-second intervals, stirring in between, until melted, about 2 minutes total. Stir in the sugar, vanilla, and coffee granules.
In a large bowl, vigorously whisk the eggs until bubbly on top, about 1 minute. Stir the eggs into the chocolate mixture. Add the flour, cocoa powder, and baking powder and stir until just combined. Stir in the remaining 0.5 cup chocolate chips. Transfer the batter to the prepared pan and spread evenly.
Bake until the brownies are just set in the center, 30 to 40 minutes. Remove from the oven and drizzle spoonfuls of the warmed peanut butter over the top, lightly spreading it in an even layer. Let the brownies cool for about 30 minutes. Using the parchment overhang, remove the brownies from the baking dish.
Meanwhile, make the frosting. In a large bowl, combine the butter, powdered sugar, melted chocolate, ¼ cup of the warm milk, the peanut butter, and vanilla. Using an electric mixer, beat until smooth, 2 to 3 minutes, adding more milk as needed until the frosting is a spreadable consistency, but is still thin enough to spread easily.
Spread the frosting over the brownies. Let set for about an hour, then slice, stack, and enjoy! Store covered at room temperature for up to 5 days.