In 1942, when Transylvania was again Hungarian, he was made bishop of the diocese of Szatmár. In 1945 the territory came under Romanian Communist rule. Scheffler could have escaped the ensuing upheaval by accepting the appointment offered him by Pius XII to succeed the assassinated William Apor as bishop of Győr in western Hungary. He, however, successfully begged the Pope to allow him to stay among his own people. 

The religious policy of the post-war Romanian Communist government was to unite the country's Eastern Orthodox church and the Latin Catholics into a single national institution, and to force the Catholics to sever their links with Rome. Scheffler refused the headship of the new church. Deep-seated hostility reigned between the Orthodox Romanians and the Hungarian Roman Catholics, so that the governmental proposal was a non-starter. 

In 1950, the communist security police detained all the un-cooperative Catholic bishops. Scheffler was first sentenced to a not particularly onerous two-year house arrest in a Franciscan convent. However, as he still refused to play the government's game, in 1952 he was moved to a prison in Bucharest and, during the last two months of his life, to the dreaded Jilava jail. He, like all the other inmates, clerics and non-clerics, had to undergo deprivation and ill-treatment and his already deteriorating health was affected. (According to some accounts, he was repeatedly subjected to showers by boiling water. According to another version, the boiling shower happened only once.) He died on December 6, 1952.

John Scheffler behaved during the last two years leading to his death as a pious, traditional Catholic prelate of his generation. If at the end, he had been set free, his memory would have survived as that of a courageous man who stuck to his convictions whatever the circumstances.  His beatification is entirely due to the fact that he ended his days in a prison of the hated regime.

In his anti-communist zeal, Pope John Paul II redefined martyrdom. According to the Oxford English Dictionary a martyr is a person who is put to death. For example, the greatest luminary of the ancient Church, Origen of Alexandria, who was severely tortured under the persecution of Decius in AD 250, but died of the ill-treatments four years later, was never recognised as a martyr. John Paul made the notion more elastic by removing execution as an essential ingredient of martyrdom. For him, it was enough that clerics, especially bishops, died in Communist jails. With the new definition in mind, Pope Benedict XVI proclaimed John Scheffler a martyr and the ceremony of beatification took place in the cathedral of Satu Mare on July 3, 2011.