Preheat oven to 350 degrees F.
Line muffin pan with muffin pan with liners or spray with baking spray.
Place beet in food processor and pulse until finely chopped. Add milk, vanilla, and honey and pulse to thoroughly mix. Add coconut oil and eggs and pulse for about 10 seconds to mix in.
In a separate bowl, combine flour, cocoa, baking powder, and salt and stir to mix. Pour liquid mixture into bowl and stir to combine.
Pour batter into prepared muffin cups, filling each about ¾ full.
Bake for 16 – 18 mins until a toothpick inserted into the middle comes out clean. Cool in pan for 10 minutes before moving muffins to a cooling rack for 20 – 30 minutes. Cupcakes must be fully cool before frosting.
To make frosting, place cream cheese, vanilla, and honey in a bowl and beat with whisk attachment on blender until smooth and creamy.
Add milk 1 tsp. at a time to thin and make desired consistency. Place in piping bag and pipe over cooled cupcakes.