Preheat oven to 375°F (190°C) and lightly grease a baking dish.
Place zucchini slices on paper towels, sprinkle with salt, and let sit for 10 minutes to draw out moisture. Pat dry.
In a large skillet, heat olive oil over medium heat. Add onion and garlic and sauté until fragrant.
Add ground beef, salt, pepper, oregano, and red pepper flakes. Cook until browned. Drain excess fat.
Stir in marinara sauce and simmer for 5 minutes.
Layer half of the zucchini slices in the baking dish. Top with half the beef sauce, half the mozzarella, and some Parmesan.
Repeat with remaining zucchini, sauce, and cheeses.
Bake uncovered for 30 minutes until bubbly and golden.
Let rest for 10 minutes before serving.