There are two ways to cook stuffed peppers. You either clean and stuff the raw pepper. You then cook it for 30 to 40 minutes at 350 degrees in the oven. You can also cook the peppers before stuffing them. Cut the pepper tops off, clean out the seeds and cook in boiling water for 5 to 7 minutes. After stuffing with the cooked ingredients, cook for 10 minutes in the oven at 350 degrees.