Make the Crust
In a bowl, mix graham cracker crumbs, cocoa powder, and brown sugar. Stir in melted butter until evenly moistened.
Line a standard muffin pan with 9 paper liners. Spoon about 1–2 tablespoons of the crust mixture into each.
Press firmly with a tablespoon or measuring cup to form an even crust. Chill while preparing the filling.
Make the Cheesecake Filling
Melt chocolate chips in a microwave-safe bowl, stirring every 20 seconds until smooth. Set aside.
Whip heavy cream in a bowl using an electric beater until stiff peaks form. Set aside.
In a large bowl, beat cream cheese and confectioners sugar until smooth. Add the melted chocolate, cocoa, coffee (if using), vanilla, and salt. Beat until fully combined.
Gently fold in the whipped cream and mix until smooth.
Divide mixture over the chilled crusts and smooth the tops.
Make the Chocolate Ganache
Heat ⅓ cup heavy cream and butter until very hot. Pour over chocolate chips and stir until melted and smooth.
Spoon ganache over each cheesecake and spread evenly. Chill for at least 4 hours or overnight.
Make Cocoa Whipped Cream
Beat heavy cream, sugar, and cocoa until stiff peaks form.
Pipe swirls on each cheesecake before serving. Garnish with shaved chocolate if desired.