Allen's sons (and his eldest daughter's widower husband) volunteered for Confederate army service. While the three eldest Allen boys and their brother in law William Watts survived the conflict (and Henry Clay Allen survived the Battle of Gettysburg), the year 1862 proved disastrous for the family. Capt. John J. Allen St. lost an arm as a result of a wound sustained at the Battle of Malvern Hill, Master sergeant George Jackson Allen died in the Seven Days' Battle and Private Baldwin Allen died of typhoid fever after his artillery unit was assigned to Tennessee.