Follow these detailed instructions to create a perfect Loaded Veggie Baked Ziti every time:

1. Preheat the Oven and Prepare Baking Dish: Preheat your oven to 375°F (190°C). Lightly grease a 9×13 inch baking dish with olive oil or cooking spray. This will prevent the ziti from sticking and make serving easier.
2. Cook the Ziti Pasta: Bring a large pot of salted water to a rolling boil. Add the ziti pasta and cook according to package directions until al dente. It’s crucial not to overcook the pasta at this stage, as it will continue to cook in the oven and you want it to maintain a pleasant texture. Once cooked, drain the pasta thoroughly and set aside. A slight drizzle of olive oil can prevent the pasta from sticking together while you prepare the vegetables.
3. Sauté the Aromatic Vegetables: While the pasta is cooking, prepare the vegetable base. Heat olive oil in a large, deep skillet or pot over medium heat. Add the chopped onion and cook until softened and translucent, about 5 minutes. Stir occasionally to ensure even cooking and prevent burning.
4. Add Garlic and Bell Peppers: Add the minced garlic and chopped bell peppers to the skillet with the onions. Cook for another 5-7 minutes, or until the bell peppers are slightly softened but still have a bit of crispness. The garlic should become fragrant, but be careful not to burn it as burnt garlic can become bitter.
5. Incorporate Zucchini and Mushrooms: Add the chopped zucchini and sliced mushrooms to the skillet. Continue to cook, stirring occasionally, until the zucchini is tender and the mushrooms have released their moisture and are starting to brown, about 8-10 minutes. This step is important to cook out excess moisture from the vegetables, preventing a watery baked ziti.
6. Stir in Spinach and Seasonings: Add the roughly chopped fresh spinach to the skillet. Cook until the spinach wilts completely, which should only take a minute or two. Once the spinach is wilted, stir in the Italian seasoning, red pepper flakes (if using), salt, and black pepper. Season generously to taste, remembering that the cheese and sauce will also contribute to the overall saltiness of the dish.
7. Combine Vegetables with Marinara Sauce: Pour the marinara sauce into the skillet with the cooked vegetables. Stir well to combine, ensuring all the vegetables are coated in the sauce. Bring the sauce to a simmer and cook for about 5-10 minutes, allowing the flavors to meld together beautifully. Simmering also helps to slightly thicken the sauce.
8. Assemble the Baked Ziti: In a large bowl, combine the cooked ziti pasta with about ¾ of the vegetable marinara sauce. Toss gently to coat the pasta evenly.
9. Layer the Ziti in the Baking Dish: Spread half of the sauced ziti mixture into the prepared baking dish. Dollop spoonfuls of ricotta cheese evenly over the ziti layer. Sprinkle about half of the shredded mozzarella cheese and half of the grated Parmesan cheese over the ricotta.
10. Add the Remaining Ziti and Toppings: Top with the remaining sauced ziti mixture. Spread the remaining ricotta cheese over the top layer of ziti. Finally, sprinkle the remaining mozzarella and Parmesan cheese evenly over the ricotta.
11. Bake to Golden Perfection: Cover the baking dish loosely with aluminum foil. Bake in the preheated oven for 20 minutes. Remove the foil and bake for another 20-25 minutes, or until the cheese is melted, bubbly, and lightly golden brown on top, and the ziti is heated through. The internal temperature should reach 165°F (74°C).
12. Rest Before Serving: Once baked, remove the ziti from the oven and let it rest for 10-15 minutes before serving. This allows the baked ziti to set slightly, making it easier to slice and serve, and also prevents burning your mouth with molten cheese!