Preheat the oven to 425°F.
Shred one medium zucchini into a mesh strainer bag, cheesecloth, or towel. Twist and squeeze all the excess liquid from the zucchini. Then discard the liquid.
Spread the shredded zucchini on a cutting board and finely dice. Measure one packed cup of shredded zucchini.
Add the bananas, cottage cheese, applesauce, maple syrup, oil, apple cider vinegar, and vanilla extract to a mixing bowl. Use an immersion blender and blend until smooth. You could also use an upright blender. This will eliminate the cottage cheese texture and banana chunks.
Add the eggs to your bowl using the whisk attachment on your immersion blender or with a hand whisk until blended.
Add the brown rice or oat flour, cocoa powder, baking powder, cinnamon, and salt to the mixing bowl. Gently whisk just until the ingredients are blended. You do not want to overmix.
Add the shredded zucchini and mini chocolate chips. Gently mix with a spatula until well combined.
Scoop the batter into a prepared muffin pan. Sprinkle with mini chocolate chips.
To get rounded tops on the muffins, bake at 425°F for 5 minutes. Leave the muffin tray in the oven, reduce the heat to 350°F, and bake for 20 minutes or until a toothpick comes out clean.
Allow to cool on the counter before removing from the muffin pan. They can be stored in the fridge for a week or frozen for several months.