After the war O'Flaherty received a number of awards, including Commander of the Order of the British Empire and the US Medal of Freedom with Silver Palm. He was also honoured by Canada and Australia. He refused to use the lifetime pension that Italy had given him.
He recruited the help of other priests (including two young New Zealanders, Fathers Owen Snedden and John Flanagan), two agents working for the Free French, François de Vial and Yves Debroise, and even communists and a Swiss count. One of his aides was British Major Sam Derry, a POW escapee. Derry along with British officers and escaped POWs Lieutenants Furman and Simpson, and Captain Byrnes, a Canadian, were responsible for the security and operational organisation. O'Flaherty also kept contact with Sir D'Arcy Osborne, British ambassador to the Holy See and his butler John May (whom O'Flaherty described as "a genius ... the most magnificent scrounger"). O'Flaherty and his allies concealed 4,000 escapees, mainly Allied soldiers and Jews, in flats, farms and convents. One of the first hideouts was beside the local SS headquarters. O'Flaherty and Derry coordinated all this. When outside the Vatican, O'Flaherty wore various disguises. The German occupiers tried to stop him and eventually they found out that the leader of the network was a priest. SS attempts to assassinate him failed. They learned his identity, but could not arrest him inside the Vatican. When the German ambassador revealed this to O'Flaherty, he began to meet his contacts on the stairs of the St. Peter's Basilica.[citation needed]
Lieutenant Colonel Herbert Kappler, the head of the SS Sicherheitsdienst and Gestapo in Rome learned of O'Flaherty's actions; he ordered a white line painted on the pavement at the opening of St. Peter's Square (signifying the border between Vatican City and Italy), stating that the priest would be killed if he crossed it. Ludwig Koch, head of the Fascist police in Rome, often spoke of his intention to torture O'Flaherty before executing him if he ever fell into his hands.[9]