He attended the University of Georgia in Athens (UGA) in the early 1840s where he was a member of the Phi Kappa Literary Society, but left before graduating.

In 1861 he was appointed as lieutenant colonel commanding the MVM's Southwest Battalion, patrolling Missouri's western border against raids by bands of Kansas Jayhawkers.

[4] In early May 1861, Bowen was ordered to St. Louis, where he took command of the new 2nd Regiment MVM, largely composed of members of the pro-secessionist Minutemen paramilitary organization.

[note 1] He was reportedly officially exchanged on November 1 and became a brigade commander, serving at Columbus, Kentucky, under Major General Leonidas Polk.

[6] After his recovery he was given a brigade command in Mansfield Lovell's division of the Army of West Tennessee and took part in the Second Battle of Corinth.

Once the army reached Ripley, Mississippi, Bowen brought charges against army commander Earl Van Dorn for failing to make a proper reconnaissance of the Union positions before the battle, "marching the troops in a hastily and disorderly manner",[7] failing to attack early on the second day, and neglecting the wounded.

At the Battle of Port Gibson, Bowen, despite being severely outnumbered, managed to delay Ulysses S. Grant's Army of the Tennessee for most of a day and he personally led two counterattacks.

Despite pleas for reinforcements, Pemberton and General Joseph E. Johnston failed to react quickly and Grant was able to resume his march through Mississippi.

[10] He took part in the final defense of Vicksburg, helping in the defeat of Union assaults, but grew ill with dysentery during the siege.

[13] His bust stands in the Vicksburg National Military Park near Stockade Redan on Graveyard Road with his brigade.