Preheat the oven to 300 degrees F (150 degrees C). Line a 12-cup muffin tin with paper liners.
Mix graham cracker crumbs, melted butter, and 2 tablespoons sugar together in a small bowl. Press 1 tablespoon of the crumb mixture into the bottom of each prepared cup.
Measure 1/2 cup chocolate chips and set aside for topping. Evenly distribute the remaining chips among the cups, sprinkling them over the crust layer.
Beat cream cheese, 1/2 cup sugar, egg, cocoa powder, and vanilla in a large mixing bowl until smooth. Spoon about 1/4 cup of the cream cheese mixture into each cup. Sprinkle remaining chocolate chips over top.
Bake in the preheated oven until just set, 17 to 23 minutes. Remove from the oven and let cool completely on a wire rack, 15 to 30 minutes.
Cover and refrigerate for at least 1 hour before serving.