After his capture the demoralized Battle was brought to Johnson's Island, effectively ending his career in the military.

[2] After being exchanged, Battle was appointed state treasurer of Tennessee, which he occupied until the end of the Civil War.

When his son Frank Battle was captured during the war, he was used as leverage by the Union side to force the return of Captain Shad Harris who was under threat of execution as a spy.

Joel Allen Battle relented and the prisoner transfer, which was endorsed by President Lincoln, took place.

Battle also had to deal with the arrest and imprisoning of his daughter Fannie along with her friend Harriet Booker in Camp Chase on suspicion of her being a Confederate spy.