When Rodes was promoted to major general and given a division in the Army of Northern Virginia, Morgan declined an offer to command Rodes's old brigade and instead remained in the Western Theater, leading troops at the Battle of Chickamauga. On November 16, 1863, he was appointed as a brigadier general of cavalry and participated in the Knoxville Campaign. His brigade consisted of the 1st, 3rd, 4th (Russell's), 9th, and 51st Alabama Cavalry regiments.