Preheat oven to 350 degrees F
In a medium bowl, sift the flour, cocoa powder, baking powder, and salt,
In a small bowl, whisk the eggs and milk.
In a large bowl, use a standing or hand mixer on medium speed to cream the sugars, butter, and applesauce. Using low speed, beat in the eggs. Slowly fold in the flour mixture.
Stir in the beet root powder and chocolate chips.
Pour the batter into 12 muffin cups, dividing evenly. Each cup should be about 3/4 full.
Sprinkle a few chocolate chips on top of each muffin cup for a richer chocolate taste.
Bake for 20-25 minutes in preheated oven, until muffins are springy to the touch. Cool in the pan for 5 minutes, then transfer to a wire rack to continue cooling.