Prep the pan and oven. Heat the oven to 375°F (190°C).
Line a 12-cup muffin tin with paper liners or grease lightly.
Mix dry ingredients. In a large bowl, whisk the flour, baking powder, baking soda, salt, cinnamon, and nutmeg until combined.
Whisk wet ingredients. In a medium bowl, whisk the eggs, brown sugar, granulated sugar, oil, yogurt, vanilla, and lemon zest until smooth.
Grate and prep the veggies. Grate the zucchini and carrot on the fine or medium side of a box grater. Place zucchini in a clean towel and gently squeeze out excess water. Don’t overdo it—just enough to stop the batter from getting watery.
Combine batter. Pour the wet mixture into the dry ingredients.
Stir gently with a spatula until barely combined and you still see streaks of flour.
Fold in veggies and add-ins. Add the zucchini, carrot, and any optional nuts or raisins. Fold just until evenly distributed. The batter will be thick but moist.
Fill the tins. Divide the batter between the 12 muffin cups.
They should be about 3/4 full. Sprinkle the tops with a little raw sugar if you like.
Bake. Bake for 18–22 minutes, or until the tops spring back and a toothpick inserted in the center comes out with a few moist crumbs.
Cool. Let muffins rest in the pan for 5 minutes, then move to a wire rack to cool. Enjoy warm or at room temperature.