Preheat the oven to 375°F. Line 2 muffin tins with paper liners. Spray with nonstick spray.
Place 3 1/2 cups zucchini in a cheese cloth or a paper towel. Squeeze out as much water as possible.
In a large bowl, whisk together 1/2 cup melted coconut oil, 3/4 cup brown sugar, 1/2 cup honey, 3 eggs, and 1 Tablespoon vanilla.
In a separate bowl, whisk together 4 cups flour, 2 teaspoons cinnamon, 1 teaspoon baking powder, 1 teaspoon baking soda, and 1 teaspoon salt. Slowly add the dry ingredients to the wet ingredients and stir with a wooden spoon just until combined, being careful not to overmix. Fold in the zucchini, 1 cup mashed bananas, and chocolate chips, if using.
Fill the muffin liners 2/3 of the way full. If adding chocolate chips, you can also sprinkle some evenly over the top of the muffins.
Bake 18 to 20 minutes, or until lightly browned and a toothpick inserted in the center comes out clean. Transfer muffins to a wire rack to cool completely.
Notes
Flour: You can use white whole wheat or kamut flour; reduce total flour by 1/2 cup for best texture. Swapping in 1 cup of oats also works well.Oil: Coconut oil can be replaced with applesauce, canola oil, or light olive oil.Add-ins: Stir in chocolate chips, chopped nuts, or dried fruit if desired.Storage: Store in a zip-top bag at room temperature up to 3 to 4 days. To avoid the muffins getting soggy, add in a few folded paper towels to absorb moisture.Freezing: Add to a freezer bag or container and store in freezer up to 2 months. To reheat, place muffin in microwave 15 to 30 seconds, or until warm.