[3] He supported Virginia's secession during the American Civil War, and all his surviving sons joined the Confederate States Army, the two youngest dying in the conflict.

In 1828, voters from the trans-Appalachian counties of Kanawha, Logan, Mason, Cabell, Randolph, Harris, Lewis and Wood elected Allen to represent them in the Virginia Senate.

After Abraham Lincoln's election in November 1860, Judge Allen called a mass meeting in Botetourt County on December 10, 1860.

He presented a resolution that he had drafted extolling Virginia's contributions to the nation's founding and condemning the north for "pharisaical fanaticism" concerning slavery and urged calling a convention to consider secession.

Allen resigned from the Court in April 1865 and retired to private life at his home, Beaverdam, near Fincastle, the Botetourt County seat.

[citation needed] Nearly three years later, his eldest son, John J. Allen Jr., won election as Botetourt County's delegate.