Heat your oven to 350 degrees F. Line 10 cups of a standard muffin pan with paper liners or lightly coat with nonstick spray. Set aside.
If using nuts for the mix-ins, toast them in the oven now: Spread the nuts into an even layer on an ungreased baking sheet. Bake at 350 degrees F for 8 to 12 minutes (for pecan or walnut halves), until they are lightly browned and fragrant. Transfer the nuts immediately to a cutting board; roughly chop and set aside.
Place the zucchini on a stack of paper towels. Pat dry and set aside.
In a large mixing bowl, whisk together the flour, oats, baking powder, baking soda, cinnamon, nutmeg, and salt.
Add the grated carrot and zucchini. Fold gently to combine.
In a separate, medium bowl, whisk together the eggs, Greek yogurt, honey, oil, and vanilla until smooth.
Add the wet ingredients to the dry ingredients, and stir gently until just combined. Do not overmix.
Fold in the nuts or any other mix-ins.
Divide the batter evenly among the 10 muffin cups. Bake for 18 to 22 minutes, or until a toothpick inserted in the center of a muffin comes out clean. Place the pan on a wire rack and let the muffins cool in the pan for 4 minutes. Gently transfer the muffins to the rack to finish cooling. Enjoy!
TO STORE: Muffins can be stored in a paper towel-lined airtight storage container at room temperature for up to 4 days.
TO FREEZE: Individually wrap each muffin, and store them in an airtight freezer-safe storage container for up to 3 months. Thaw and enjoy muffins as desired.