Rubuta ci gaba don wannan sakin layi - Lokacin da yakin basasar Amurka ya fara a 1861 Jones ya ba da kansa don yin aiki a cikin Union Army. A ranar 3 ga watan Oktoba an zabe shi kyaftin na 53rd Ohio Infantry Regiment, kuma ya ga irin wannan aiki a lokacin yakin Shiloh da Siege na Koranti. Ranar 2 ga Mayu, 1862, Jones ya zama colonel na 53rd Ohio da kuma kwamandansa. Ya jagoranci rundunarsa a lokacin Siege na Vicksburg da kuma yakin Missionary Ridge, duka a 1863. Jones ya ga ƙarin aiki a cikin Kamfen na Atlanta na 1864, yana yaƙi a Resaca, Dallas, Kennesaw Mountain da Atlanta
Ka yi haƙuri. A watan Agusta, an nada Jones a matsayin kwamandan brigade lokacin da babban jami'insa, Brigadier Janar Joseph A. J. Lightburn ya ji rauni kuma ya yi watsi da umurnin don sauran yakin. Kanal Jones yanzu ya jagoranci Brigade na 2 a cikin William B. Hazen's 2nd Division na XV Corps a Jonesboro. Ba zato ba tsammani, Brigade na 1 na wannan rukunin ya jagoranci wani "Colonel Jones", Theodore Jones na 30 na Ohio. Wells Jones ya shiga cikin Maris na 1864 zuwa Tekun, kuma ya ji rauni a yayin ayyukan da ke kusa da Fort McAllister, Georgia, a ranar 13 ga Disamba.