Preheat oven to 350 degrees. Line a metal 9x9 baking pan with aluminum foil, leaving an overhang on the sides to lift the finished brownies out. Spray the foil with non-stick cooking spray.
In a large mixing bowl, whisk together the cocoa powder, sugars, salt, gluten free flour, and chocolate chips.
Add the eggs, oil, and water to the mixing bowl and stir until combined.
Using a rubber spatula, fold in the peanut butter cups.
Transfer the batter to the prepared pan and smooth out.
Drop tablespoons of peanut butter on top of the brownie batter. Using a table knife, draw lines through the batter, vertically and then horizontally, to create a swirled design.
Bake for 25-30 minutes. Check the brownies after 25 minutes by gently shaking the pan. If the brownie wobbles in the middle, continue to bake for another 5 minutes.
Place the pan of baked brownies on a wire rack to cool completely. Cut into squares and enjoy!