Begin by boiling or roasting your beets. Once beets are cooked, simply cut in half and place in food processor. Process until beets are pureed. Add applesauce to beet puree and pulse several times to combine.
Add oil to beet mixture and stir (or pulse) to combine. In a large bowl, combine sugar, flour, cocoa, baking soda, baking powder, and salt. Whisk to combine.
Add beet mixture to flour mixture and stir just until combined. Stir in vanilla. Add chocolate chips and stir gently to distribute. Divide batter into 12 lined or sprayed muffin cups. Bake at 400 degrees for 18-20 minutes.
Allow muffins to cool for several minutes in the pan, then remove and cool completely on a rack. Enjoy!