Following Solidarity's victory in the parliamentary election in June 1989, Poland resumed diplomatic relations with the Holy See on 17 July 1989. On 26 August 1989, Pope John Paul II nominated Kowalczyk as the first post-war apostolic nuncio to Poland. The pope consecrated him as titular archbishop of Heraclea in St. Peter's Basilica on 20 October 1989. Kowalczyk chose the words Fiat Voluntas Tua as his episcopal motto; his episcopal coat of arms is charged with a cross, a pastoral staff, a star symbolizing the Blessed Virgin Mary, and a plough symbolizing Kowalczyk's rural origin. The nuncio arrived in Warsaw on 23 November 1989 and presented his letter of credence to President Wojciech Jaruzelski on 6 December 1989. at the Presidential Palace in Warsaw As nuncio, Kowalczyk presided over the reëstablishment of the military ordinariate of Poland in 1991. Together with the Conference of Polish Bishops, he worked on a thorough reorganization of the administrative structure of the Catholic Church in Poland. This task resulted in the papal bullTotus Tuus Poloniae populus of 1992, which erected 13 new dioceses, elevated eight dioceses to archdioceses, and adjusted ecclesiastical borders to match the post-war borders of Poland. The nuncio also negotiated with Polish authorities the text of the concordat which was signed on 28 July 1993 and ratified by Poland in 1998. The concordat, in which the Republic of Poland agreed, among other things, to recognize the legal personality of the Catholic Church and legal validity of church marriages, became a model for other concordats in Europe and for regulations on Poland's relations with other denominations. Kowalczyk was also responsible for preparing John Paul II's and Benedict XVI's papal visits to Poland in 1991, 1995, 1997, 1999, 2002, and 2006. By tradition, Kowalczyk – in his capacity as the apostolic nuncio – acted as dean of the diplomatic corps in Poland. Although formally he was not part of the Conference of Polish Bishops, he played an important advisory role. His job was also to propose candidates for episcopal appointments to the Holy See; during his 21-year-long nunciature – the longest ever in a single country – Kowalczyk had a considerable influence on the composition of the Catholic episcopate in Poland.
Primate of Poland
On 8 May 2010, Pope Benedict XVI accepted the resignation of retiring Archbishop Henryk Muszyński and nominated Kowalczyk as the new archbishop of Gniezno and primate of Poland. He was ceremoniously installed at the Gniezno Cathedral on 26 June 2010. The primatial title, which is traditionally held by the head of the oldest archbishopric in Poland, no longer carries significant power in national or church structures, but remains a prestigious honorific post. On 17 May 2014, Kowalczyk retired as Pope Francis accepted his resignation from the archiepiscopal see of Gniezno and appointed Archbishop Wojciech Polak as his successor.