Begin by preheating your oven to 350°F (175°C). Prepare a muffin tin by lining it with paper liners or greasing it lightly with cooking spray.
In a medium mixing bowl, combine the grated zucchini, vegetable oil (or applesauce), eggs, and vanilla extract. Whisk until smooth and uniform.
In a large mixing bowl, sift together the all-purpose flour, whole wheat flour, packed brown sugar, granulated sugar, baking soda, baking powder, sea salt, and ground cinnamon.
Gently pour the wet ingredients into the dry ingredients. Fold together just until combined, being careful not to overmix.
Fold in the semi-sweet chocolate chips, reserving a small handful for topping.
Spoon the batter into the prepared muffin tin, filling each cup about two-thirds full. Sprinkle reserved chocolate chips on top.
Place the muffin tin in the oven and bake for 18-20 minutes until a toothpick comes out clean or with a few moist crumbs.
Remove from the oven and let cool in the tin for 5 minutes before transferring to a wire rack to cool completely.
Notes
For an elegant touch, serve warm with powdered sugar or cream cheese frosting.