Preheat oven to 350 degrees F. Line a 12-cup muffin tin with liners and coat with non-stick cooking spray.
Add the following ingredients to a food processor or blender: oats, eggs, yogurt, beets, Truvia, milk, oil, and vanilla. Blend 2-3 minutes, until smooth.
In a large bowl, combine flour, cocoa powder, baking soda, and salt. Whisk to combine. Pour wet mixture into dry mixture. Mix until just combined; avoid overmixing. Fold in chocolate chips (reserve a few for sprinkling on top of the muffins). Divide batter evenly among prepared muffin cups. Sprinkle with any remaining chocolate chips. Bake for 20 minutes, or until a toothpick inserted in the center comes out mostly clean. Transfer to a wire rack to cool.