In a large bowl, whisk together the flour, sugar, cocoa, baking soda, and salt.
In a small bowl, beat the milk, oil, egg and vanilla extract. Add to the flour mixture and stir until just combined. Stir in half of the chocolate chips and allow the batter to rest.
Preheat oven to 350ºF.
Once the oven is preheated, fill the muffin cups about half full with the chocolate cake batter.
With the remaining cake batter and all of the cream cheese batter, spoon equal amounts of each on top of the cake batter, creating a top that is half chocolate and half cream cheese. Do Not Over Fill.
Sprinkle each of the cupcakes with a few of the remaining chocolate chips.
Bake for 30 to 35 minutes or until a cake tester inserted into the center comes out clean.
Place the muffin tin on a wire rack to cook for 10 minutes.
After the 10 minutes are up, take the cupcakes out of the pan to cool completely on the wire rack.
Store refrigerated in an airtight container. Bring to room temperature before serving for optimal flavor.