Morgan was transferred to the Army of the Ohio (later the Army of the Cumberland). He commanded a brigade in George Thomas's Center Wing, but during the Stones River Campaign the division he belonged to was left behind to guard Nashville. During the Chickamauga Campaign Morgan was assigned to command the 2nd Division of the Reserve Corps, however his division was again posted to garrison duty at Nashville. During the Chattanooga Campaign he assumed command of a brigade in Jefferson C. Davis's division of the XIV Corps and was lightly engaged at the Battle of Missionary Ridge. He led his brigade during the Atlanta Campaign. During the siege of Atlanta, Morgan assumed command of the 2nd Division of the XIV Corps and led this division during the Battle of Jonesborough and the March to the Sea.