After attending the minor seminary in Culemborg from 1898 to 1904, de Jong then studied at the Seminary of Rijsenburg for four years. He was ordained to the priesthood on August 15, 1908, and further studied at the Pontifical Gregorian University and the Angelicum in Rome, obtaining his doctorates in philosophy and theology.
He served as Archbishop of Utrecht from 1936 until his death, and was elevated to the cardinalate in 1946 by Pope Pius XII.
Becoming the seminary"s rector on August 14, 1931, he was named a canon of the cathedral of Utrecht in 1933. On August 3, 1935, de Jong was appointed Coadjutor Archbishop of Utrecht and Titular Archbishop of Rhusium. He received his episcopal consecration on the following September 12 from Bishop Pieter Hopmans, with Bishops Arnold Diepen and Johannes Smit serving as co-consecrators, in Saint Catherine"s Cathedral.
De Jong succeeded Johannes Henricus Gerardus Jansen as Archbishop of Utrecht and thus Primate of the Netherlands.
He was also the first archbishop in the Netherlands with a university degree since the restoration of the Dutch Catholic hierarchy in the middle of the 19th century. He said he didn"t want to be another Innitzer and ordered his priests to refuse the sacraments to Nazi Dutchmen.
During the Second World War, he was one of the major leaders against the Nazi occupation of Netherlands. On July 26, 1942 Dutch bishops, including Archbishop Johannes de Jong, issued a decree that openly condemned Nazi deportations of Dutch workers and Jews.
The Nazis retaliated by seizing over 40,000 Catholics of Jewish descent, including Edith Stein.
The Vatican used the Netherlands" experience to explain its silence during the years of the Holocaust. After the German retaliation, Sister Pasqualina Lehnert, Pius XII"s housekeeper and confidante, said the Pope was convinced that while the Bishop’s protest cost forty thousand lives, a protest by him would mean at least two hundred thousand innocent lives that he was not ready to sacrifice. While politicians, generals, and dictators might gamble with the lives of people, a Pope could not.
De Jong was created of South. Clemente by Pope Pius XII in the consistory of February 18, 1946, but could not travel to Rome for the ceremony as he was recovering from a car accident.
However, on October 12 of that year, the Dutch prelate went to Castel Gandolfo to receive his red hat from Pope Pius. Meanwhile, de Jong retired to the same house where he had lived during his early priestly ministry in Amersfoort.
De Jong died in his sleep after a long illness in Amersfoort, two days before his 70th birthday. He is buried at Saint Barbara cemetery in the court of Saint Catherine"s Cathedral.