Bee was posted after the war to garrison duty at Pascagoula, Mississippi, where he served as adjutant. From 1849 to 1855, he was on frontier duty in New Mexico. He was stationed primarily at Fort Fillmore near Las Cruces, New Mexico. In 1855, Bee was promoted to captain of Company D of the Tenth Infantry and posted to Fort Snelling, Minnesota. While at Fort Snelling, he met and married Sophia Elizabeth Hill, the sister of a fellow officer. In 1857, Bee's company took part in the Utah War, which involved confrontation with members of the Church of Latter Day Saints, also known as Mormons. He was placed in command of the Utah Volunteer Battalion and brevetted to the rank of lieutenant colonel. In 1860, Bee was posted to Fort Laramie, Wyoming, where he briefly served as the fort's commanding officer.