Preheat the oven to 350 degrees F. Grease muffin tins.
Peel, slice and cook the apple
Cook the thoroughly clean beets, in 1/3 of a cup of water, until just tender. Save the coloured beet water, hold the beets under cold water and slip off the skins with your fingers. Add the roughly chopped beets and cooked apple to the blender. Process until finely chopped.
Add the oil, sugar, milk and eggs to the blender and process until just mixed.
In a large bowl sift flour, cocoa, baking powder, baking soda and salt. Add the beet mixture, and mix with a spoon until just combined.
Fill the muffin tins two-thirds full, with batter.
Bake 20-25 minutes, or until a toothpick inserted in the center comes out clean. Allow the cupcakes to cool in the pans for about 5 minutes. Remove the muffins and cool on a cake rack.