He was an 1831 honors graduate of the United States Military Academy, where he was an assistant professor for two terms, in addition to his duties as a second lieutenant in the 1st U.S.

[1] Within a week after the Confederate bombardment of Fort Sumter in April 1861, Ammen rejoined the Federal army, serving as a captain in the newly raised 12th Ohio Infantry.

After training at Camp Chase, Ammen's regiment was sent in late July to serve in western Virginia, seeing their first combat at the Battle of Cheat Mountain.

Shipped to the Western Theater, Ammen led a brigade in the Army of the Ohio at the Battle of Shiloh and the Siege of Corinth.

When his health deteriorated, Ammen then performed administrative duty for nearly a year, commanding Camp Douglas in Illinois in early 1863, as well as other Federal garrisons.