In a small mixing bowl, whisk together the all-purpose flour, unsweetened cocoa powder, baking soda, and granulated sugar.
Add in the egg, vegetable oil, water, apple cider vinegar, and vanilla extract. Mix until just combined. The batter will be on the thinner, runnier side.
Using a 1 ½ tablespoon-size cookie scoop (or 2 spoons), fill the cupcake liners no more than ½ full, then top with a spoonful of the chocolate chip cream cheese filling. If desired, add a few more semi-sweet mini chocolate chips to the top.
Bake for 22-24 minutes at 350ºF.
Remove from the oven and cool for 10 minutes in cupcake tin. Then transfer to wire rack and allow to cool completely.
Keep cupcakes stored in an airtight container in the refrigerator for up to 5 days. They can be enjoyed chilled or at room temperature.