Prepare the pizza crust according to the instructions.
While the crust is baking, heat the olive oil in a large skillet over medium heat. Add the onion, peppers, and mushrooms. Sauté the veggies until soft, 5-7 minutes. Transfer to a plate while the crust finishes baking.
When the crust is done baking, remove it from the oven and top it with the sauce. Layer on the sautéed veggies. Bake for 12-15 minutes until the veggies are steaming and starting to char slightly. Let cool for 5 minutes before slicing. Sprinkle with nutritional yeast (if using) and serve.