Preheat your oven to 325°F (163°C). Line a 12-cup muffin tin with paper liners.
In a mixing bowl, combine melted butter and sugar until smooth.
Add the egg and vanilla extract and whisk until fully incorporated.
Fold in the cocoa powder and flour until a thick brownie batter forms.
Divide the brownie batter evenly among the muffin cups.
Bake for 10 minutes to par-bake the brownie layer.
While the brownies bake, beat the cream cheese and sugar until smooth and creamy.
Add the egg and heavy cream, then mix until fully combined and silky.
Remove the muffin tin from the oven and gently pour the cheesecake mixture over each brownie base.
Return to the oven and bake for 18 minutes, or until the cheesecake edges are set and the centers are slightly jiggly.
Cool to room temperature, then refrigerate for at least 4 hours.
To prepare the ganache, melt the dark chocolate with heavy cream until smooth and glossy.
Drizzle the ganache over the chilled Brownie Bottom Cheesecake Bites.
Sprinkle with mini chocolate chips before serving.