He was posted to garrison duty in Arkansas and then transferred to Mississippi where his regiment was attached to Andrew J. Smith's division in the XVI Corps during the Meridian expedition.

Gilbert won the commendation of his brigade commander, Colonel William T. Shaw, for his performance at the battles of Fort DeRussy and Pleasant Hill.

In June, 1864 Gilbert assumed command of the 2nd Brigade, 3rd Division, XVI Corps and led it at the battle of Tupelo.

On December 5, 1864, Gilbert was transferred to command of the 2nd Brigade, 2nd Division in Smith's detachment of the Army of the Tennessee (formerly XVI Corps) at the battle of Nashville.

For a time he went to Colorado as a miner then moved to Kansas to become president of the Topeka Coal Economizing Company.