Preheat the oven to 350°F. Grease a 9x13-inch baking dish with cooking spray or line with parchment paper and set aside.
In a medium bowl, make peanut butter batter by beating cream cheese, peanut butter, sugar, egg, and milk. Mix until smooth.
In another bowl, make the brownie batter by mixing sugar, melted butter, and vanilla until combined. Add eggs, one at a time, beating until well combined.
In another bowl, combine flour, cocoa, baking powder and salt. Mix until combined and then add to the wet ingredients of the brownie batter. Stir until combined, and then fold in chocolate chips.
Scoop out ½ cup of brownie batter and set aside.
Spread the remaining brownie batter into the prepared baking dish. Carefully pour the peanut butter mixture over the brownie batter. In spoonfuls, drop the reserved brownie batter over the top of the peanut butter layer. With a knife, gently swirl the top layers, inserting the knife a little into the batter and swirling up and down to create a marbled effect.
Bake for 35-40 minutes, or until a toothpick inserted into the middle comes out clean. Sprinkle with some flaky sea salt if desired. Let cool completely before cutting into bars.