Prep the pan: Preheat oven to 350°F (175°C). Line a mini muffin pan or a standard muffin pan with liners, or lightly grease with nonstick spray.
Grate the zucchini: Use the small holes on a box grater.
Lightly blot the grated zucchini with a paper towel to remove excess moisture, but don’t squeeze it dry. You want it damp, not dripping.
Mix the wet ingredients: In a large bowl, whisk the egg, applesauce, oil, both sugars, and vanilla until smooth.
Add the zucchini: Stir the grated zucchini into the wet mixture until evenly distributed.
Combine the dry ingredients: In a separate bowl, whisk the flours, baking powder, baking soda, salt, cinnamon, and nutmeg (if using).
Bring it together: Add the dry mixture to the wet mixture. Stir gently with a spatula just until no dry streaks remain.
Do not overmix.
Optional add-ins: Fold in nuts or mini chocolate chips if you like, noting this will increase the calorie count.
Fill the cups: For mini muffins, fill each cup about 3/4 full. For standard muffins, aim for just over 1/2 full to keep them smaller than a typical bakery muffin.
Bake: Mini muffins bake for 10–12 minutes; standard muffins bake for 14–16 minutes. They’re done when a toothpick comes out clean or with a few moist crumbs.
Cool: Let muffins rest in the pan for 5 minutes, then transfer to a wire rack to cool completely.
This helps them set and stay fluffy.