He commanded a brigade in Stonewall Jackson's Valley Campaign, and was badly wounded at Gaines Mill, ending his active field career.

Artillery and sent to Florida to fight in the Second Seminole War before being assigned to duty at Detroit, Michigan, during a series of territorial disputes between the U.S. and Canada.

He also participated in engagements at Fort Brown, Vera Cruz, Cerro Gordo, Molino del Rey, Chapultepec, and the capture of the City of Mexico.

He resigned his commission on April 25, 1861, and traveled to Richmond, Virginia, where he joined the Confederate army with the initial rank of colonel of the newly formed 1st Maryland Infantry, CSA.

[6] Later relieved of command, he raised the Local Defense Brigade, a militia group consisting primarily of government clerks.

[3]: 83 In June 1864, Elzey left Richmond to join General Jubal Early's force defending Lynchburg, Virginia.

Elzey was assigned as the Chief of Artillery for the Army of Tennessee and traveled to Georgia to serve under John Bell Hood.

With Hood's army essentially wrecked, Elzey was relieved of duty on February 17, 1865, and then assumed command of militia at Augusta, Georgia.