Preheat oven to 350 degrees Fahrenheit and spray muffin pan with nonstick oil.
Puree sliced beets, berries and mint leaves until smooth, reserve a cup of mix for used in the topping.
Mix spelt flour, egg and berry mixture in a large bowl until well combined.
Spoon mix into the molds.
Bake for 20 to 25 minutes, until a toothpick inserted in the middle come out clean.
Cool 5 minutes in pan then remove and place on wire racks to cool completely.
Topping
In a bowl combine the cream cheese and cup of berry mix until smooth.
Fill piping bag with topping and pipe on top of pupcakes.
Decorate with mint leaves if desired.
