Gather the ingredients. Preheat the oven to 375 degrees F (190 degrees C). Lightly grease a 7x11-inch casserole dish.

Layer sliced squash, zucchini, onion, and tomatoes in the baking dish, sprinkling with cheese and adding pats of butter between each layer of vegetables, and seasoning with salt and ground black pepper to taste. Continue layering process until vegetables are used up; top with remaining butter and cheese.

Cover the casserole and bake in the preheated oven until vegetables are to desired tenderness and cheese is melted and bubbly, about 20 to 30 minutes.