Preheat oven to 400°F. Grease a 12-cup muffin tin or line with muffin liners. Set aside.
In a large mixing bowl, whisk together the all-purpose flour, wheat flour, salt, baking soda, baking powder, cinnamon, and nutmeg. Add the mini chocolate chips and toss to combine with the flour mixture. Set aside.
In a separate bowl, whisk together the eggs, Greek yogurt, oil, honey, vanilla, and mashed banana.
Add the wet ingredients to the dry ingredients and stir to combine.
Add the shredded zucchini (no need to drain it). Stir to combine.
Spoon muffin batter into each muffin cup, filling 2/3 full.
Bake for 5 minutes. Reduce oven temperature to 375°F and bake an additional 18-22 minutes, until a toothpick inserted into the center comes out clean. Remove from oven and place pan on a wire cooling rack. Allow to cool for 5 minutes before removing muffins from pan. Continue cooling muffins on rack. Serve and enjoy!