Preheat oven to 375 degrees F. Grease muffin tins with oil or non-stick spray (or line with cupcake wrappers).
In a bowl combine, beet puree, eggs, sugars, oil, and milk until smooth.
In another bowl whisk together flour, cocoa, baking soda and salt until combined. Fold in liquid ingredients until just moistened. Add chocolate chips.
Pour into prepared muffin tins, about ⅔rds full. Bake for 15-18 minutes. Let cool in pan for a few minutes before moving to a cooling rack to cool completely.
Notes
*To prepare beet puree: clean and trim 1-2 large beets, wrap in aluminum foil and bake at 350 degrees for approximately 15-20 minutes until beet is soft. Clean off peel using the foil, roughly chop then puree in food processor or blender, adding a small amount of water as needed, to blend until completely smooth. If using canned beet, use part of the liquid in lieu of water to puree.