- On July 6, 1947 Pope Pius XII appointed Archbishop de Jonghe d’Ardoye “Apostolic Delegate in the Indonesian Archipelago” and on the following day the Apostolic Letter to erect the Apostolic Delegation “in the Indonesian Archipelago” was issued. Three weeks after his appointment, on Sunday July 27, 1947, Archbishop de Jonghe d’Ardoye arrived by plane in Batavia. On August 6, 1947 the Apostolic Delegate gave the Lieutenant General of the Dutch East Indies, Hubertus Johannes van Mook, the letter of presentation signed by Mgr Tardini.
- On January 4, 1950, the Holy See gave instructions to its Representative to convey that it recognized the Republic of the United States of Indonesia. Two days later Mgr de Jonghe d’Ardoye personally informed the Vice-President and Foreign Minister Hatta about this decision; the latter requested him to ask the Holy See to establish diplomatic relations with Indonesia. On January 10, 1950 the Holy See informed Jakarta that it had accepted the proposal, that an Internunciature in Indonesia would be established and that it would receive a Legation to the Holy See.
- On March 16, 1950 it was announced that “The Holiness of our Lord has been pleased to erect the Apostolic Internunciature in the United States of Indonesia, located in Jakarta, deigning at the same time to appoint as Apostolic Internuncio His Excellency Mgr Georges de Jonghe d’Ardoye, titular Archbishop of Misthia” (L’Osservatore Romano, March 17, 1950). On receiving his Credential Letters, the new Internuncio was able to present them to President Sukarno on April 6, 1950, in the State Palace.
- On May 25, 1950 Ambassador Sukardjo Wirjopranoto, the Envoy Extraordinary and Minister Plenipotentiary of the Republic of the United States of Indonesia presented his Letters of Credence to Pope Pius XII.
- On June 13, 1956, President Sukarno was received in audience by Pope Pius XII, who conferred the Pian Order on him. Sukarno returned to the Vatican on May 14, 1959, and was received by John XXIII; on that occasion, the President invited the Pope to visit Indonesia. The other two visits of the Indonesian President took place on June 15, 1963 (during the sede vacante following the death of John XXIII) and on October 12, 1964, when he met Pope Paul VI.
- On January 3, 1961 Pope John XXIII issued the Apostolic Constitution “Quod Christus”, establishing the Catholic hierarchy in Indonesia. Six Ecclesiastical Provinces were created (Jakarta, Semarang, Ende, Medan, Pontianak and Makassar) and the existing Apostolic Vicariates and Apostolic Prefectures became Archdioceses and Dioceses. The execution of the Apostolic Constitution was entrusted to the then Apostolic Internuncio, Archbishop Gaetano Alibrandi.
- On December 7, 1966 the Apostolic Internunciature in Indonesia was elevated to the rank of Apostolic Nunciature. On the same date, Archbishop Salvatore Pappalardo was appointed Apostolic Pro-Nuncio to Indonesia.
- In 1966 the Legation of Indonesia to the Holy See became an Embassy. On May 16 the Minister Plenipotentiary Isa Mohamad Nazir presented the Letters accrediting him as Ambassador to Pope Paul VI.
- That same year, on June 1, the new building of the Apostolic Nunciature was inaugurated. The construction of the new building of the Papal Representation had been initiated in October 1964 by Archbishop De Liva and was carried out in accordance with plans drawn up by the German architect Hermann Bohnenkamp. The formal inauguration of the new building took place on June 29, 1966, at which President Sukarno was present.
- At the Consistory of June 26, 1967 Pope Paul VI created Mgr Justinus Darmojuwono, Archbishop of Semarang, Cardinal Priest with the title of the Most Holy Names of Jesus and Mary in Via Lata: he was the first Indonesian Cardinal. After him, at the Consistory of November 26, 1994, John Paul II created Mgr Julius Darmaatmadja, Archbishop of Semarang, Cardinal Priest with the title of the Sacred Heart of Mary.
- On December 3, 1970, during his visit to Asia and Oceania, Paul VI visited Indonesia. He arrived in Jakarta from Sydney and was greeted by President Suharto; the Pope then met the priests and religious in the cathedral of the capital. After a stop at the Nunciature and a courtesy call to the President of the Republic, the Pope celebrated Holy Mass in the capital’s stadium, before departing for Hong Kong. At that time the Papal Representative was Archbishop Joseph Mees.
- During his Apostolic Visit to the Far East and Mauritius (October 6-16, 1989), Pope John Paul II visited Indonesia from October 9 to 14. Besides visiting Jakarta, he also visited Yogyakarta, Maumere, Dili and Medan. In the capital the Pope met the Bishops, the civil authorities, religious leaders, the clergy and religious, and the world of culture. During those days the Pope stayed at the Apostolic Nunciature, which at that time was led by Archbishop Francesco Canalini.
- After the independence of East Timor from Indonesia (2002), the Apostolic Nunciature which was established in that country on June 23, 2003 was entrusted to the Papal Representative in Jakarta; this remained the case until 2011.
- From 2007 to 2010, extensive restoration and extension works were carried out in the residence of the Apostolic Nunciature. On October 11, 2009 Archbishop Leopoldo Girelli inaugurated the new chapel dedicated to the Twelve Apostles.
- On June 18, 2011 Benedict XVI appointed Archbishop Leopoldo Girelli, Apostolic Nuncio to Singapore, as Apostolic Nuncio to the Association of South-East Asian Nations (A.S.E.A.N.), which has its headquarters in Jakarta.