Preheat the oven to 350°F. Line a cupcake tin with liners.
Make a flax egg: combine the 4 teaspoons of ground flax with ¼ cup water. Set aside.
In a medium bowl, mix the oat flour, almond flour, beetroot powder, cocoa powder, baking powder, baking soda, and salt. Set aside.
In a separate, large bowl, whisk the flax egg, applesauce, maple syrup, nut butter, apple cider vinegar, and vanilla.
Slowly stir the dry ingredients into the wet.
Scoop the batter into the lined muffin tin. Fill each cup ¾ of the way full. You may have 1-2 cupcakes worth of extra batter - don't overfill the cups. Gently shake the pan for 30 seconds to help the batter settle.
Bake for 17-20 minutes, until a toothpick inserted into the center of the cupcake comes out clean. Remove from the oven and let cool completely.
Meanwhile, prepare the cream cheese frosting. Using a hand mixer or stand mixer beat the frosting ingredients until combined and slightly fluffy. Refrigerate until ready to use.
When the cupcakes are cooled, spread frosting onto each cupcake. Enjoy!