Prep and Crust: Preheat your oven to 300°F. In a medium bowl, combine the fine graham cracker crumbs, sugar, cocoa powder, and melted butter. Press the mixture firmly into the bottom and halfway up the sides of a 9-inch springform pan.
Cream the Base: In a stand mixer or large bowl, beat the softened cream cheese and 1/4 cup sugar until light and fluffy. Gradually pour in the sweetened condensed milk, beating until fully incorporated.
Incorporate Peanut Butter: Add the melted peanut butter chips to the mixture and beat until the batter is smooth and uniform in color.
Add Eggs and Vanilla: Beat in the eggs one at a time, ensuring each is fully mixed before adding the next. Stir in the vanilla extract last. Pour the batter into the prepared cocoa crust.
The Water Bath: Place your springform pan inside a larger roasting pan. Fill the larger pan with hot water until it reaches halfway up the side of the springform pan (wrap the bottom of the springform in foil first to prevent leaks!).
The Bake: Bake for 60–70 minutes. The edges should be set, but the center should still have a slight jiggle and a matte finish.
Cooling Process: Remove from the oven and immediately run a thin knife around the edge of the pan. Let it cool completely on a wire rack at room temperature.
The Ganache Finish: Heat heavy cream in a saucepan until it simmers. Pour the hot cream over the chocolate morsels in a glass bowl. Let it sit for 2 minutes, then whisk until glossy. Pour over the cooled cheesecake and spread evenly.
Chill: Refrigerate until the ganache is set and the cheesecake is cold (at least 4–6 hours, preferably overnight).