Preheat oven to 375°F (190℃).
Bring a large pot of salted water to a boil. Add your ziti pasta and cook for 6 minutes, or until al dente. Drain and set aside. Your pasta will be slightly undercooked. Don't worry, it will finish cooking in the oven.
While the pasta is cooking, make your vegan ricotta cheese (or use store-bought). Set aside.
In a large saucepan, heat the olive oil over medium heat. Add the diced onion and sauté for 5 minutes, or until the onion is translucent.
Add the vegan beef crumbles to the pan and saute for a further 3 minutes.
Add the minced garlic and sauté for another minute.
Add the crushed tomatoes, tomato sauce, dried basil, dried oregano, red pepper flakes, salt, and pepper to the saucepan. Bring the sauce to a simmer and cook for 10-15 minutes, stirring occasionally.
Add the cooked ziti pasta to the saucepan and stir until the pasta is coated in sauce.
In a 9x13 inch baking pan, spread half of the pasta and sauce mixture. Dollop the the vegan ricotta cheese on top of the pasta
Add the remaining pasta and sauce mixture on top of the first layer. Sprinkle with vegan Mozzarella.
Cover the pan with foil and bake for 40 minutes.
Remove the foil from the pan and bake for 20 more minutes.
Allow the vegan ziti bake to rest uncovered for 10 minutes before serving.