Preheat the oven to 190°C (375°F).
In a large oven-safe pot or Dutch oven, heat the olive oil over medium heat.
Add the chopped onion and sauté for 3-4 minutes until translucent.
Add the minced garlic and cook for 1 minute until fragrant.
Add the diced red bell pepper, zucchini, and sliced mushrooms to the pot. Cook for 5 minutes, stirring occasionally, until the vegetables start to soften.
Add the penne pasta, canned diced tomatoes (with juice), vegetable broth, dried oregano, dried basil, chili flakes, salt, and black pepper. Stir well to combine all ingredients.
Bring the mixture to a simmer, then cover the pot with a lid.
Transfer the covered pot to the preheated oven and bake for 25 minutes, or until the pasta is cooked and most of the liquid is absorbed.
Remove the pot from the oven and stir the pasta gently.
Sprinkle the shredded mozzarella and grated Parmesan evenly over the top.
Return the pot to the oven uncovered and bake for an additional 5-7 minutes, or until the cheese is melted and golden.
Remove from the oven and let it rest for 5 minutes before serving.
Garnish with fresh basil leaves and serve warm.