Maney asked for a reassignment to his native Tennessee, which was threatened by Union forces. As an officer in the Army of Tennessee, Maney participated in the Battle of Shiloh and was promoted on April 16, 1862, to brigadier general. He led his brigade in the battles of Perryville, Chickamauga, and Murfreesboro. In November 1863, he was wounded severely in his arm during the Chattanooga Campaign. He was on medical leave for much of the rest of the year.