Preheat the oven to 325°Line an 8×8-inch metal baking pan with parchment paper or foil, leaving an overhang. Spray with nonstick cooking spray.
In a large bowl combine the butter, sugar, cocoa powder, and salt. Stir until well combined, mixture will be thick. Let cool if the butter is still hot.
Stir in the vanilla and then the eggs, one at a time, stirring very well after each addition. Stir until the batter is very well blended. Add the flour and stir again until very well blended. The mixture will be thick. Spread into prepared pan.
Bake for 15 minutes, or until just starting to set but not fully cooked. Maintain 325°F oven temperature.
Make the cheesecake:
While the brownies are baking, make the cheesecake batter. In a large bowl, use an electric mixer to beat the cream cheese, peanut butter, and sugar until well combined and smooth, scraping down the sides and bottom of the bowl often to incorporate everything smoothly. Beat in the eggs, flour, and salt just until incorporated.
Pour the cheesecake batter over the partially baked brownie layer.
Bake at 325°F for about 40 to 45 minutes, or until the cheesecake is set.
Cool completely to room temperature before refrigerating for at least 4 hours to chill.
Make the peanut butter ganache:
Place the cream in a glass measuring cup. Microwave for 25 seconds, or until steaming hot but not bubbling. Add in the chocolate chips and peanut butter. Let sit for 2 minutes. Stir until smooth. Let cool at room temperature until thickened but still pourable.
Spread the ganache all over the chilled cheesecake layer. Refrigerate for 15 minutes, or until the ganache is fudgy.
Cut into bars. For clean cuts, use a big sharp knife and run it under hot water and wipe it off between slices. Bars can be stored in an airtight container in the fridge for up to 3 days.