Preheat and prep. Heat your oven to 400°F (200°C).
Lightly grease a 9x13-inch baking dish with olive oil.
Season the chicken. Pat the chicken dry. Season generously with salt, pepper, and 1 teaspoon Italian seasoning. If breasts are thick, slice them in half horizontally so they cook evenly.
Sauté the aromatics. In a skillet over medium heat, warm 1 tablespoon olive oil.
Cook onion with a pinch of salt until softened, 3 to 4 minutes. Add garlic and cook 30 seconds, until fragrant. Stir in the marinara and a pinch of red pepper flakes if using.
Simmer 2 minutes, then remove from heat.
Dress the zucchini. In a bowl, toss zucchini slices with 1 tablespoon olive oil, a pinch of salt, pepper, and the remaining 1 teaspoon Italian seasoning. This helps them keep some texture.
Layer the bake. Spread a thin layer of sauce in the baking dish. Arrange the seasoned chicken in a single layer.
Spoon half the remaining sauce over the chicken. Scatter the zucchini evenly on top. Pour the rest of the sauce over the zucchini.
Add cheese. Sprinkle half the mozzarella and half the Parmesan over everything.
Reserve the rest for later so the top gets golden without overbrowning too soon.
Bake covered. Cover loosely with foil and bake for 20 minutes. This helps the chicken cook through and the zucchini soften without drying out.
Uncover and finish. Remove the foil. Add the remaining mozzarella and Parmesan.
Bake another 10 to 15 minutes, until the cheese is melted and bubbly and the chicken reaches an internal temperature of 165°F (74°C).
Broil for color. If you like a browned top, broil for 1 to 2 minutes. Watch closely so it doesn’t burn.
Rest and garnish. Let the bake rest for 5 to 10 minutes. Finish with chopped basil or parsley and a drizzle of olive oil.
Serve warm.