Sauté the onion and garlic with olive oil in a large skillet over medium heat; cook until the onions are soft and transparent.
Slice the zucchini, yellow squash, and tomato into ¼-inch slices.
Coat the inside of an casserole dish with non-stick spray.
Spread the sautéed onion and garlic in the bottom of the dish. Arrange the other sliced vegetables, stacked vertically, in an alternating pattern. Season the top of the vegetables generously with salt, pepper, and dried oregano.
Cover the dish with foil and bake in the preheated oven for 30 minutes.
Remove the foil, top with the shredded cheese, and bake without the foil for an additional 15 minutes.
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