The army saw little action the rest of 1862 and Butler was replaced by Major General Nathaniel P. Banks on December 17.

The army endured the siege and the post was finally surrendered by Confederate forces on July 9, 1863.

The XIX Corps was sent to the Shenandoah Valley, and the forces that remained in the army participated in the land attack at the Battle of Mobile Bay.

Late in the war, Maj. Gen. Edward Canby's Military Division of West Mississippi was given the army's two remaining corps, the XIII and the XVI, for a planned offensive to capture the city of Mobile.

During this operation, Canby renamed the force the Army of West Mississippi after the military division that he commanded.