On December 19, 1942, Stroud was transferred to Alcatraz Federal Penitentiary, and became inmate #594. He reportedly was not informed in advance that he was to leave Leavenworth and his beloved birds, and was given just 10 minutes' notice of his departure. His birds and equipment were sent to his brother as Alcatraz's strict policies meant that he was unable to continue his avocation. He spent six years in segregation and another 11 confined to the hospital wing at the penitentiary.