Preheat the oven to 375F (190C) and line a 12 cavity muffin pan with muffin papers. This recipe will yield 12-14 muffins, so you may need 2 pans.
Lightly blot the grated zucchini with paper towel to remove excess liquid. You do not need to remove all the liquid. Do not try to squeeze the zucchini dry. Set aside.
In a large bowl, whisk together the flour, cinnamon, nutmeg, baking powder, baking soda and salt. Set aside.
In a separate large bowl, whisk together the oil, brown sugar, granulated sugar, eggs, vanilla extract and milk until there are no lumps.
Make a well in the middle of the dry ingredients and pour the wet ingredients into the well.
Gently fold the mixture together - I do this with a rubber spatula to help avoid overmixing.
When the mixture is about 80% combined, stir in the grated zucchini. As you stir in the grated zucchini any remaining clumps of flour will stir out.
Carefully fold in the chocolate chips.
Spoon the batter into the prepared muffin tin filling each paper about ¾ of the way full. You should end up with 12-14 muggins in total.
Bake 1 tray at a time in the middle of your oven for about 22-25 minutes, or until an inserted toothpick comes out clean or with a few crumbs. If an inserted toothpick comes out with muffin batter, the muffins are not done baking yet.
Cool the muffins in the pan for about 10 minutes, then carefully transfer to a cooling rack to continue cooling.