Step 1

Adjust oven rack to middle position and heat oven to 375 degrees. Brush 13 by 9-inch baking dish with 1 tablespoon oil; set aside.

Step 2

Heat 2 tablespoons oil in 12-inch nonstick skillet over medium heat until shimmering. Add onions and 1/2 teaspoon salt and cook until softened and lightly browned, 12 to 15 minutes. Stir in garlic and cook until fragrant, about 30 seconds. Spread onion mixture on bottom of prepared dish.

Step 3

Alternately shingle zucchini, yellow squash, and tomatoes into single layer of 4 tightly fit rows on top of onions. Sprinkle with thyme, drizzle with remaining 1 tablespoon oil, and season with salt and pepper. Cover dish with aluminum foil and bake until vegetables are tender, about 30 minutes.

Step 4

Remove foil, sprinkle Gruyère over top, and continue to bake until bubbling around edge and lightly browned on top, 20 to 30 minutes longer. Let rest for 10 minutes before serving.