Gather all ingredients. Preheat the oven to 400 degrees F (200 degrees C).

Bake pie crust in preheated oven until firm, about 8 minutes. Remove crust from the oven and set aside. Reduce oven to 350 degrees F (175 degrees C).

Heat olive oil in a large skillet over medium heat. Add onion, bell pepper, mushrooms, and zucchini and cook, stirring, until softened, 5 to 7 minutes. Remove vegetables from skillet and set aside.

Sprinkle tomato slices with flour and basil; cook in the skillet over medium heat for 1 minute per side. Set aside.

Whisk eggs, milk, salt, and pepper together in a small bowl.

Spread 1 cup cheese in the bottom of pie crust. Layer vegetable mixture over the cheese, then top with tomato slices. Pour egg mixture over top and sprinkle with remaining 1/2 cup cheese.

Bake in the preheated oven until a knife inserted near the center comes out clean, 40 to 45 minutes.

Cool 5 minutes before serving.