Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease the cups.
In a medium bowl, whisk together the all-purpose flour, unsweetened cocoa powder, baking soda, baking powder, and salt until well combined.
In a large bowl, beat the granulated sugar, light brown sugar, and eggs together until smooth and creamy.
Add the vegetable oil and vanilla extract to the sugar and egg mixture and mix until fully incorporated.
Fold the dry ingredients into the wet ingredients until just combined, being careful not to overmix.
Gently fold in the grated zucchini and mini chocolate chips until evenly distributed throughout the batter.
Divide the batter evenly among the 12 muffin cups, filling each about 3/4 full.
Bake in the preheated oven for 18 to 20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Remove the muffins from the oven and allow them to cool in the tin for 5 minutes, then transfer to a wire rack to cool completely.