Preheat the oven to 350 degrees F (175 degrees C). Grease a 2-quart baking dish with cooking spray.

Mix together zucchini, onion, muffin mix, beaten eggs, salt, and pepper in a large bowl until well combined. Stir in 4 ounces cheese. Spread evenly into the prepared baking dish. Sprinkle with remaining 4 ounces cheese.

Bake in the preheated oven until the top is lightly browned and a toothpick inserted into the center comes out clean, about 60 minutes.