Preheat oven to 350 degrees Fahrenheit (175 degrees Celsius) and line a standard 12-cup muffin tin with paper liners.
In a medium mixing bowl, whisk together the whole wheat flour, cocoa powder, baking soda, and sea salt until well combined.
In a large mixing bowl, beat the egg, maple syrup, applesauce, and vanilla extract until the mixture is uniform.
Fold the shredded and drained zucchini into the wet ingredient mixture.
Gradually incorporate the dry ingredients into the wet ingredients, stirring until just combined; do not overmix.
Gently fold in the dark chocolate chips.
Divide the batter evenly among the 12 muffin cups, filling each approximately three-quarters full.
Bake for 18 to 22 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Cool the muffins in the tin for 5 minutes before transferring to a wire rack for complete cooling.