Prep: Preheat oven to 400 degrees. Line a standard muffin pan with paper or silicon liners, set aside.
Use a cheese grater and shred 1 large zucchini to obtain the 1 cup, as well as 1-2 medium size carrots. Squeeze the extra moisture from the zucchini with a paper towel.
Batter: In a large bowl, combine flour, wheat and oat flour, salt, baking soda, baking powder, cinnamon, and nutmeg. Mix to combine. Add in the eggs, oil, apple sauce, yogurt, honey, and vanilla extract. Stir again to combine all ingredients well.
Lastly, add in the shredded zucchini and carrots, pecans, and raisins (if desired), mix until just blended. Proceed to pour the batter into the prepared muffin cups about ¾ of the way full.
Bake: Place the muffins into the preheated oven and bake for 18-20 minutes for regular sized muffins, or 12-14 minutes for mini-muffins. Let them cool for about 10 minutes before taking out of muffin tins. Serve and enjoy!