Preheat the oven to 350℉. Line the muffin tins with liner or cooking spray.
Shred the zucchini. Press as much moisture out of the zucchini as you can with paper towels or a kitchen towel. Transfer the zucchini to a fine mesh sieve to continue draining while you prepare the muffin batter.
In a large mixing bowl, combine flour, cocoa powder, baking powder, baking soda, and salt. Mix to combine.
In another large mixing bowl, whisk together eggs, zucchini, maple syrup, almond milk, applesauce, coconut oil, and vanilla extract.
Make a well in the dry ingredients and pour in the wet ingredients. Mix to combine. Don't overmix the batter. You can have a few streaks or bumps of flour in the batter. Fold in ½ cup of chocolate chips.
Spoon the batter into the prepared muffin tin, filling all the way full. You can top with the remaining ¼ cup of chocolate chips, if desired. Bake 18 to 22 minutes, or until a toothpick inserted into the center comes out mostly clean with a few crumbs (there shouldn't be any batter on the toothpick).
Allow the muffins to cool in the muffin tins on a wire rack for 5 minutes. Transfer the muffins to the cooling rack to finish cooling. Enjoy!