In Cork, Lynch re-organised the Irish Volunteers—the paramilitary organisation that became the Irish Republican Army (IRA)—in 1919, becoming commandant of the Cork No. 2 Brigade of the IRA during the guerrilla Anglo-Irish War. Lynch helped capture a senior British officer, General Cuthbert Lucas, in June 1920, shooting a Colonel Danford in the incident. Lucas later escaped while being held by IRA men in County Clare. Lynch was captured, together with the other officers of the Cork No. 2 Brigade, in a British raid on Cork City Hall in August 1920.