Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease the cups.
Grate the zucchini using a box grater. Place grated zucchini in a clean kitchen towel and squeeze out excess moisture. Set aside.
In a large bowl, whisk together the eggs, granulated sugar, brown sugar, vegetable oil, and vanilla extract until smooth and combined.
In a separate medium bowl, sift together the gluten free flour blend, cocoa powder, baking powder, baking soda, and salt.
Gradually add the dry ingredients to the wet ingredients, stirring gently until just combined. Do not overmix.
Fold in the grated 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 18 to 20 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, then transfer to a wire rack to cool completely.