Line a standard muffin pan with 9 paper baking cups.
In a medium bowl, whisk together the gluten-free flour, baking powder, baking soda, salt, cinnamon and nutmeg.
In a large bowl, whisk together the eggs, sugar, oil and vanilla until well-combined.
Add the dry ingredients to the wet mixture and stir with a rubber spatula until just combined.
Lightly squeeze the zucchini to get out some of the excess liquid. (You don’t need to overdo it, just reduce some of the moisture.) Stir in the shredded zucchini and chocolate chips, if using, until just combined.
Using a kitchen scoop or large spoon, fill 9 paper baking cups all the way up. (I find I can usually make 9 full muffins with this batter, but you could also make 12 smaller muffins.)
Refrigerate the muffins for 20 minutes before baking. Preheat the oven to 400°F.
Bake the muffins for 10 minutes at 400°F, then reduce the oven temperature to 350°F and continue to bake for 10-15 minutes, until the tops are lightly browned and a toothpick inserted into the center comes out clean.
Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.