Preheat your oven to 350°F. While it heats, dice the onion and green pepper into 1/2-inch pieces, mince the garlic, and crumble or slice the vegan sausage into bite-sized pieces. Having everything prepped and ready will make the cooking process smooth and prevent anything from burning while you're chopping.

Bring a large pot of salted water to a boil and cook the mostaccioli according to package directions until just al dente (don't overcook—it will continue cooking in the oven). Drain the pasta and set aside. I prefer to reserve about 1/2 cup of pasta water just in case the final dish seems too dry, but it's optional.

In a large skillet or Dutch oven, heat the olive oil over medium heat. Add the diced onion and green pepper, cooking for 6-8 minutes until softened and just starting to caramelize at the edges. Stir in the minced garlic and red pepper flakes, cooking for 1 minute until fragrant. This layering of aromatics builds a deeper, more complex flavor foundation for the dish.

Add the crumbled vegan sausage to the pan with the sautéed vegetables and cook for 5 minutes, stirring occasionally to break it up and allow it to brown slightly. This develops more flavor and texture compared to adding it raw to the sauce.

Add the cooked mostaccioli from Step 2 to the pan with the sausage mixture, then pour in the marinara sauce and stir everything together until well combined. Season generously with salt and pepper to taste. I find that this dish needs a bit more seasoning than you might expect since the pasta tends to absorb flavors—taste as you go and adjust before baking.

Transfer the pasta mixture to a 9x13 inch baking dish, spreading it evenly. Top with the vegan mozzarella cheese, distributing it so the whole dish gets covered. Cover the dish tightly with foil and bake for 15 minutes, then remove the foil and bake uncovered for another 15 minutes until the cheese is melted and the edges are bubbling. The foil traps steam initially to keep everything moist, while removing it at the end allows any excess moisture to evaporate and the cheese to set.

Remove the baking dish from the oven and let it rest for 3-5 minutes before serving. This brief rest allows the dish to set slightly and makes serving much easier.