Preheat oven to 350 degrees.
Prepare a muffin pan by spraying with non-stick spray or insert muffin liners.
In a large bowl, stir together the flours, sugar, cocoa powder, baking soda, salt, and the cinnamon. Set aside.
In a separate bowl, whisk together the egg, applesauce, vegetable oil, milk, and the vanilla extract.
Pour the wet ingredients into the dry ingredients until just combined, do not over mix.
Fold in the zucchini and the chocolate chips.
Pour the batter evenly in the muffin pan.
Bake the muffins for 20-25 minutes or until a toothpick inserted comes out clean.
Remove the muffins from the pan and let them cool.