Start by preheating the oven to 425 degrees Fahrenheit. Grate 2 cups of carrots and set aside.
In a large mixing bowl place the eggs, oil, milk, and vanilla. Whisk together until well combine.
Place the cocoa powder, whole wheat flour, sugar, baking powder, baking soda, salt, in a bowl. Whisk everything together until well combine.
Pour the egg mixture, chocolate chips, and carrots into the flour mixture. Use a spatula to fold the batter together just until combine, about 12 -15 folds.
In a greased muffin pan, fill each cup all the way up (about ⅓ cup each). Sprinkle each muffin with a few more chocolate chips. Bake for 8 minutes, then turn the oven to 375 degrees Fahrenheit and bake for another 5-7 minutes. Until they are not gooey inside. Let them sit in the muffin pan for 5 minutes before removing them.