Bagwell became an independent member of Seanad Éireann in the Irish Free State in 1922, and held that office until 1936. During the Irish Civil War he was kidnapped and held hostage by Republicans in the Dublin Mountains. The Free State government responded by issuing a proclamation to the effect that if he was not safely released, reprisals would be taken. He maintained that he escaped his captors through his own efforts and his safe release could not be attributed to these threats. At about this time the family residence of Marlfield House, Clonmel, County Tipperary was burned by Anti-treaty forces and the library of rare historical documents destroyed.