As the overall health of the regiment continued to improve, the 2nd Iowa was ordered to guard McDowell College. After the owner of the college joined the Confederate army, the U.S. War Department seized the school and converted it into a military prison. When the 2nd Iowa began guarding the prison, there were approximately 1,300 prisoners held at the college. Thanks to some reeducation and the resulting oaths of allegiance, the number was reduced to approximately 1,100 prisoners at the time of the 2nd Iowa's departure. Colonel Tuttle led the re-education of the prisoners, teaching the rebels “Uncle Samuel is not to be fooled with and that prisoners have to submit or somebody will get hurt.” Shortly before the 2nd Iowa would be relieved of prison duty in early 1862, a few unknown members of the regiment broke into a museum at the college and stole some items of minimal importance. Because of this, General Henry Halleck ordered that the regiment, which was well-liked by the people of St. Louis and the prisoners, march through the streets on the way to the steamer T. H. McGill in disgrace without music or colors. On February 10, 1862, the 2nd Iowa Infantry embarked on their next assignment.