Gather the ingredients. Preheat the oven to 350 degrees F (175 degrees C). Grease two 12-cup muffin tins or line with paper cups.

Beat cream cheese, egg, 1/3 cup sugar, and 1/8 teaspoon salt in a medium bowl until light and fluffy. Stir in chocolate chips; set aside.

Mix together flour, 1 cup sugar, cocoa, baking soda, and 1/2 teaspoon salt in a large bowl. Make a well in the center; add water, oil, vinegar, and vanilla. Stir together until well blended.

Fill the prepared muffin tins about 1/3 full with chocolate batter. Top each with a dollop of cream cheese mixture.

Bake in the preheated oven until a toothpick inserted into the chocolate cake comes out clean and the cream cheese center is set, 25 to 30 minutes.