Preheat oven to 350F (175C) and line two 12-count muffin tins with paper liners. Set aside.
Prepare cream cheese filling first by stirring together cream cheese and sugar until well-combined and not lumpy. Stir in egg, salt, and vanilla extract until completely combined.
Stir in chocolate chips. Set aside.
To prepare chocolate batter:
In a large bowl, whisk together flour, sugar, cocoa powder, baking soda, and salt.
Add milk, oil, vinegar, and vanilla extract and stir until batter is smooth and well combined.
Evenly divide chocolate batter into prepared muffin tins, filling each liner only ⅓ full with batter.
Dollop 1 ½ Tablespoons of cheesecake batter onto the top of the chocolate batter in the center.
Transfer to 350F (175C) oven and bake for 16-18 minutes.
Allow to cool and then enjoy.
¹I mentioned that this is my grandmother's recipe, but I did deviate in one way. Her recipe called for 1 cup water. After a lot of taste testing I decided I liked it best with 1 cup of milk instead.This recipe can be made into mini black bottom cupcakes. Fill liners of mini cupcake tin less than ½ full of chocolate batter then dollop 1-1 ½ teaspoons of cream cheese filling on top.Bake about 14-16 minutes. Will make 48 mini black bottoms.
I prefer these black bottoms when they are stored in the refrigerator (something about liking my cheesecake cold!). Make sure you store them in an airtight container so they don’t dry out!