Bring a large pot of salted water to a boil over high heat. Add the penne and cook it until very al dente, about 2-3 minutes less than the package instructions. Reserve 1 cup of the pasta water, then drain the penne and set it aside.

In the same oven-safe skillet, heat a couple of tablespoons of extra virgin olive oil over medium heat. Add the chopped yellow onion, cooking until translucent and slightly sweet, about 5-7 minutes. Mix in minced garlic and optional red pepper flakes, sautéing for another minute until fragrant.

Stir in crushed tomatoes and vegetable broth (or reserved pasta water). Sprinkle in dried oregano, dried basil, salt, and black pepper. Bring to a gentle simmer and let it bubble for about 10 minutes.

Fold in the fresh spinach, stirring until wilted. Reduce heat to low and add ricotta, half of mozzarella, and half of Parmesan. Stir until well combined.

Gently incorporate the al dente penne into the sauce, ensuring every piece is coated.

Preheat your oven to 375°F (190°C). Sprinkle remaining mozzarella and Parmesan evenly on top. Cover tightly with aluminum foil and bake for 20 minutes. Then remove foil and bake for an additional 10-15 minutes until cheese is golden and bubbly.

Remove from oven and let it rest for about 5 minutes before serving.