Heat the olive oil in a pan, sauté the onions, garlic and bell pepper until the onions are glassy. Set aside.
Cook the pasta al dente. In a large pot, heat the rest of the oil and stir in the flour. Cook, while stirring, until the \\\\\\\"floury\\\\\\\" smell is gone. Add the soy milk, vegan cheese and stir until the cheese has melted, bring to a low boil. Season with salt and nutmeg, fold in the vegetable and then the pasta.
Place mixture in a casserole dish and bake at 180° C for 25-30 min, until the sauce is bubbly and the top has a golden crust. This dish is best when served immediately!