Preheat the oven to 400°F (200°C). Place the oven rack in the center position. Line a muffin tin with paper liners and spray the inside of the liners with cooking spray.
In a large mixing bowl, add the flour, unsweetened cocoa powder, baking powder, and salt. Stir until evenly combined.
Shred the zucchini. Use a clean, dry cloth (or paper towels) to squeeze out as much excess liquid from the shredded zucchini as you can. Set the drained zucchini aside.
In a medium mixing bowl, whisk together the melted coconut oil, brown sugar, vanilla extract, eggs, and milk until smooth and combined.
Pour the wet ingredients into the dry ingredients. Add the drained shredded zucchini and the mini chocolate chips.
Stir the batter gently just until the ingredients are combined and no large streaks of flour remain. Do not overmix.
Divide the batter evenly among the prepared muffin cups.
Bake for 20–22 minutes, or until a toothpick inserted into the center of a muffin comes out clean or with just a few moist crumbs.
Remove the muffins from the oven. Let them cool in the pan for a few minutes, then transfer the muffins to a cooling rack and let cool for a few more minutes before serving.