Bowen served as a captain of the Missouri militia and a chief of staff to General D. M. Frost during the war. He was captured at Camp Jackson. However, he was exchanged and, subsequently, he organized the 1st Missouri Infantry, of which he was appointed colonel. He was promoted to brigadier general in March 1862. He participated in the Battle of Shiloh, in which he was wounded. He quickly was back in action during the Vicksburg campaign, participating in the Battle of Port Gibson. In May 1863, he received the rank of major general. He served throughout the battle preceding the siege of Vicksburg, but, after the surrender, he died due to ill health as a paroled prisoner.
