Preheat the oven to 350˚F (180˚C) and line a muffin tin with 12 paper liners. Spray the liners with non-stick cooking spray.
Prepare the grated carrot and zucchini. Squeeze the grated zucchini over a bowl or strainer with your hands to squeeze out the excess liquid. You should have a compressed ball of grated zucchini when it's ready.
In a large bowl, mix the drained zucchini, carrot, applesauce, coconut sugar, maple syrup, coconut oil, ground flax and almond milk until well combined.
Add the flour, baking powder, baking soda, cinnamon, nutmeg and salt and gently mix until "just combined". Do not overmix the batter or the muffins will be tough. Gently mix in the walnuts and raisins if using.
Spoon batter into the 12 muffin liners and sprinkle a few chopped walnuts on top of each if desired. Bake 18-20 minutes, or until a toothpick inserted into the middle of a muffin comes out clean and the tops are golden brown. Bake times may vary depending on your oven.
Remove muffins from the oven when done and let sit for at least 5 minutes in the pan before transferring to a wire rack to finish cooling.