Preheat the oven to 375 degrees F. Line a muffin tin with liners.
In a large bowl, make the flax egg by combining the ground flaxseed and water. Stir and set aside to thicken.
In a medium bowl, add the flour, baking powder, baking soda, salt, cinnamon, and nutmeg. Whisk until combined.
In the large bowl with the flax egg, add the zucchini, coconut sugar, almond milk, applesauce, maple syrup, vanilla, and apple cider vinegar. Whisk until well combined.
Add the dry mixture to the wet. Stir with a rubber spatula until combined. Careful not to overmix. Fill muffin tins all the way full, this helps you get big fluffy muffins. Bake for 17-18 minutes or until toothpick comes out clean. Let it sit in the pan for 5 minutes then remove muffins and place on a wire rack to cool completely. Enjoy! Store in an airtight container. The liners peel off better when the muffins are completely cooled and have sat covered in an airtight container overnight.