After Alabama
declared secession, Allen enlisted in the newly raised Confederate States Army and was elected as a
lieutenant in Company A, Montgomery Mounted Rifles. The following year, when the state organized the 1st Alabama Cavalry, Allen became its first major on March 18, 1862. He saw action at the
Battle of Shiloh in April along the
Tennessee River. He was subsequently promoted to colonel of the
regiment before the
Kentucky Campaign and led the 1st Alabama Cavalry at the
Battle of Perryville, where he received a slight wound. Later that year, he was severely wounded in the
Battle of Murfreesboro while in command of a
brigade. Out of action for over a year while recuperating from surgery which left him little use of his right hand, Allen returned to field duty in early 1864. On February 26 of that year, he was promoted to
brigadier general and took command of a brigade of cavalry at
Dalton, Georgia. His brigade was composed of the 1st, 3rd, 4th, 9th, 12th, and 51st Alabama Cavalry regiments, and they served in the
corps of
Joseph Wheeler in the Army of Tennessee. Allen led the brigade throughout the Alabama Campaign. In August, a Georgia cavalry brigade was added to Allen's force and, later, Anderson's Brigade. Allen, now in charge of a full
division, participated in the
Atlanta campaign in the summer, as well as contesting
Sherman's March to the Sea (Savannah Campaign). Although
Confederate President Jefferson Davis appointed him a
major general in February 1865, the
Confederate States Congress did not confirm his promotion before it was dissolved. In early 1865, Allen's Division fought in the
Carolinas campaign. Allen and his men surrendered at
Concord, North Carolina, on May 3. He was paroled shortly thereafter as a brigadier general. ==Postbellum career==