Bring a large pot of salted water to a boil. Add the pasta and cook until al dente, about 8 minutes. Drain well and set aside.
While the pasta cooks, heat a tablespoon of olive oil in a skillet over medium. Add chopped garlic and onion, sautéing until fragrant and translucent, about 3 minutes.
Add chopped vegetables to the skillet and cook until tender, about 5-7 minutes, stirring occasionally. The mixture should be fragrant and slightly caramelized.
In a mixing bowl, combine the cooked vegetables, tomato sauce, nutritional yeast, and season with salt and pepper. Mix thoroughly until well combined.
Add the drained pasta to the bowl with the sauce mixture, folding gently to coat each piece evenly.
Transfer the coated pasta mixture into a deep baking dish, spreading it out evenly.
Toss the breadcrumbs with a tablespoon of olive oil and sprinkle them evenly over the top of the pasta. Add a little more nutritional yeast if desired for extra cheesy flavor.
Bake in a preheated oven at 180°C (350°F) for 20-25 minutes, until bubbling around the edges and the breadcrumb topping is golden brown.
Remove from the oven and let rest for 5 minutes. Garnish with fresh herbs or a drizzle of olive oil if desired.
Serve hot and enjoy this cozy, cheesy-inspired vegan pasta bake with a side salad or crusty bread.