Preheat oven to 350°F. Line a standard size muffin tin (12 wells) with large or oversized cupcake liners. Set aside.
In a large bowl or an 8-cup measuring cup, sift together the flour, baking soda, salt and cocoa. Whisk in the sugar.
Whisk the egg, coffee/water, vegetable oil, vanilla and vinegar into the dry dry ingredients until just mixed. Do not overmix. Set aside for 10-15 minutes.
Vanilla Cream Cheese Batter:
In a separate mixing bowl or bowl of a stand mixer fitted with the paddle attachment, beat the cream cheese until smooth, approximately 2-3 minutes.
Add the sugar, vanilla and egg until fully incorporated and glossy. Fold in 1/2 cup of the mini chocolate chips by hand.
Evenly divide the chocolate batter between the wells. Evenly divide the cream cheese mixture to each well. Evenly divide the remaining 1/4 cup of mini chocolate chips between each cupcake. Wells will be full.
Bake for 20 minutes, or until tops spring back slightly. Do not allow to brown. TUrn off the oven and crack the oven door for 10-15 minutes.
Remove and cool fully before serving or transfering to the refrigerator for storage.
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