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 gluten free flour, cocoa powder, baking powder, baking soda, and salt until well combined.
In a large bowl, beat the granulated sugar, brown sugar, and eggs together until smooth and creamy.
Add the vegetable oil and vanilla extract to the egg mixture and mix until combined.
Gradually add the dry ingredients to the wet ingredients, stirring gently until just combined. Do not overmix.
Fold in the shredded zucchini and mini chocolate chips until evenly distributed.
Divide the batter evenly among the 12 muffin cups, filling each about 3/4 full.
Bake for 22 to 25 minutes, or until a toothpick inserted into the center of a muffin comes out clean or with a few moist crumbs.
Remove the muffins from the oven and allow them to cool in the pan for 5 minutes.
Transfer the muffins to a wire rack to cool completely before serving.