Preheat the oven to 375°F (190°C). Spray a 12-cup muffin tin with nonstick spray or line with muffin liners and set aside.
In a large bowl, whisk together the all-purpose flour, unsweetened cocoa powder, granulated sugar, packed light brown sugar, baking powder, baking soda, and salt until evenly combined.
In a separate bowl, whisk the egg, melted unsalted butter, vanilla extract, and skim milk until smooth.
Add the wet ingredients to the dry ingredients and stir until just combined; do not overmix.
Fold in the finely shredded zucchini and semisweet chocolate chips until evenly distributed; the batter will be thick.
Divide the batter evenly among the prepared muffin cups, filling each about 3/4 full.
Bake for 20–25 minutes, or until a toothpick inserted into a muffin center comes out clean or with a few moist crumbs.
Remove the pan from the oven and let the muffins cool in the pan about 10 minutes, then transfer to a wire rack to cool completely.