He also served as a military officer during the Mexican–American War and the American Civil War. In 1828, after the death of his first wife and dissolution of the utopian experiment at New Harmony, Owen traveled for a few years, farmed in Lancaster County, Pennsylvania, and lived in Cincinnati, Ohio, where he briefly worked in a brewery, before returning to New Harmony in 1836 to operate a steam-powered flour mill and manage a livestock farm. In 1848 Owen began assisting his brother, David Dale Owen, who was appointed as Indiana's first state geologist, in performing geological work in the Northwest Territory. In the summer of 1849 Owen assisted his brother in conducting a geological survey of northern Minnesota and the shores of Lake Superior. Owen's duties primarily consisted of recording atmospheric pressure measurements and making illustrative sketches. Later that year Owen accepted a professorship in natural science at the Western Military Institute in Kentucky. He remained a member of the school's faculty until 1859 and an owner of the institute with Bushrod Johnson, who later became a general in the Confederate States Army. During Owen's tenure at the school, it was relocated to Tennessee and merged with the University of Nashville. In addition to teaching at the university, Owen published one of his major works, "Key to the Geology of the Globe" (1857) and received a Doctor of Medicine degree from the Medical College of Nashville in 1858. Prior to the outbreak of the American Civil War and largely because of his anti-slavery opinions, Owen resigned his position and sold his financial interest in the Institute in 1858. After his return to Indiana, Owen was appointed assistant state geologist and helped his brother, David Dale Owen, with surveys of the central part of the state. When David died in 1860, Richard Owen succeeded him to become Indiana's second state geologist. Richard Owen also completed and published David Owen's second geological survey of Indiana,"Report of a geological Reconnaissance of Indiana" (1862). As a result of his promotion to state geologist, Owen became an "ex officio" member of the Indiana University faculty at Bloomington, Indiana. and was serving as the state geologist of Indiana when the American Civil War began in 1861. Owen, a pro-Union Democrat, joined the Union army and served as a lieutenant colonel in the 15th Indiana Infantry Regiment and fought in the battles of Rich Mountain, Greenbrier River, and Cheat Mountain. Owen was promoted to colonel after the Battle of Greenbrier River and reenlisted in the 60th Indiana Infantry Regiment, where he remained until December 1863.