For the cupcakes:

1. Preheat oven to 350 degrees F. Line cupcake pan with paper liners and coat with baking spray.
2. Place beets in food processor and pulse until finely chopped. Measure out 1 cup of chopped beets and save the remaining for future use. Return one cup beets to food processor (or high-speed blender), add kefir, Greek yogurt and vanilla and process until pureed.
3. In a large mixing bowl, add flour, baking powder, baking soda, cocoa powder and salt and whisk to combine.
4. In a stand mixer, or using an electric hand mixer, beat butter and sugar until fluffy, about 5 minutes. Beat in eggs, one at a time. Add flour mixture and beet mixture alternatively, starting and ending with flour.
5. Spoon batter into prepared cups. Bake 15 to 20 minutes, or until toothpick inserted in center comes out clean. Remove cupcakes from pan and let cool completely on wire rack.

For the frosting:

1. In a medium mixing bowl, add cream cheese, Greek yogurt and butter. Using an electric hand mixer, beat until smooth. Add powdered sugar and beat until just combined. Spread frosting evenly over cooled cupcakes.