Preheat oven to 450°F (230°C).
Heat 1/4 cup olive oil in a large oven-safe skillet over medium heat.
Add onion, garlic, salt, and pepper. Cook for 3–4 minutes until softened.
Stir in oregano and red pepper flakes; cook for 1 minute until fragrant.
Add crushed tomatoes and simmer for 6–8 minutes until slightly thickened.
In a bowl, mix breadcrumbs, 1/3 cup Parmesan, remaining olive oil, salt, and pepper.
Stir beans and remaining Parmesan into the sauce and cook for 2 minutes.
Taste and adjust seasoning.
Top with mozzarella, then evenly sprinkle breadcrumb mixture.
Bake for 15 minutes until golden and bubbly.
Let rest for 5 minutes and garnish with fresh basil before serving.
This Beans Parmesan Bake is best served hot with crusty bread or a fresh salad.