Peel, cut and boil 2 medium sized beets until tender. Drain beets reserving ~1/3 cup of water. Add beets to a food processor and puree adding 1 tablespoon at a time until an applesauce consistency is achieved.
To make Cupcakes:
Preheat oven to 350 degrees F. Line a mini-cupcake pan with paper cups and set aside. In a large bowl whisk together beet puree, oil, milk and sugar. In a separate bowl sift together flour, baking powder, salt and cocoa powder. Mix dry ingredients into wet ingredients. Spoon into cupcake cups until 3/4 full. Bake for 15-20 minutes or until a toothpick inserted comes out clean. Let cool.
To make Cinnamon Cream Cheese Frosting:
In a large bowl using a hand held mixer beat together cream cheese, butter and vanilla. Gradually add in powdered sugar and cinnamon. Blend until creamy. Spread on cooled cupcakes and enjoy!