Preheat oven to 350 degrees. Spray the inside of a 9×13 inch baking pan.
In a medium size bowl whisk the dry ingredients together, flour, salt and cocoa powder.
Place butter and chocolate chips in a microwave safe bowl. Cook for 30 seconds and stir. Repeat until chocolate chips are melted. Whisk in sugars and stir until combined.
Add the eggs to the chocolate mixture, one at a time, stirring well between each addition. Stir in vanilla. Sprinkle the flour mixture over the chocolate mixture and fold in the dry ingredients with a rubber spatula until just combined. Fold in remaining chocolate chips from the bag.
Pour the batter into 9×13 pan and press the Reese’s peanut butter cups into batter. Bake until a toothpick inserted into the center of the brownies comes out with a few moist crumbs, about 30 minutes.
Let cool completely in the pan. Cut into squares and serve at room temperature.