Preheat the oven to 350°F (180°C).
Line 12 muffin cups with liners or lightly grease them.
Whisk brown rice flour, almond flour, potato starch, baking soda, baking powder, salt, and ground nutmeg in a large bowl.
Wash very well and grate the zucchinis on the large holes of a box grater. Place the zucchini on a clean towel and squeeze to press out as much moisture from the zucchini as possible. Add the zucchini to the flour and mix with a rubber spatula.
Mix the eggs with the sugars, oil, lemon zest, and vanilla extract. Add to the flour mixture and mix with a rubber spatula until well incorporated.
Pour the mixture into the prepared pans. Fill the muffins 3/4 full, dividing as evenly as possible.
Bake for 25/30 minutes. To know if it’s ready insert a toothpick into the center of the muffin, it should come out clean, with no streaks of batter.
Let cool before removing.