Preheat oven to 350˚F. Line cupcake pans with 18 paper liners.
In a small bowl, combine first five ingredients and mix well. Add chocolate chips and crushed peppermint and stir to combine. Set aside.
Mix sugar, flour, cocoa, baking soda and salt and stir to combine. In a separate bowl, combine water, oil, vinegar and vanilla . Add wet ingredients to the bowl of dry ingredients and stir until well combined.
Fill prepared muffin tins ½ full with this mixture.
Drop a rounded tablespoon of cheese mixture on top, dividing mixture evenly. Bake for 23 to 25 minutes. Cover for last 8-10 minutes if getting too brown. Don't under bake or your cupcakes will sink in the center.
Allow to cool in the pan for five minutes, then transfer to a cooling rack. Cool completely before icing.