Preheat the oven to 350°F (175°C). Grease two 12-cup muffin pans or line them with paper liners.
Make the cheesecake filling:In a medium bowl, beat cream cheese, egg, ⅓ cup sugar, and ⅛ tsp salt until smooth and creamy. Stir in the chocolate chips. Set aside.
Make the chocolate batter:In a large bowl, whisk flour, 1 cup sugar, cocoa powder, baking soda, and ½ tsp salt.Then make a well in the center and add the water, oil, vinegar, and vanilla.Stir until fully combined (the batter will be thin).
Assemble:Fill each muffin cup ⅓ full with the chocolate batter.After that, spoon some of the cream-cheese mixture on top of each portion.
Bake:Bake for 25–30 minutes, or until the chocolate layer is set and a toothpick inserted into the cake portion comes out clean.
Cool:Let the cupcakes cool in the pan for a few minutes, then transfer them to a wire rack to cool completely.
