He was ordained priest by auxiliary bishop Józef Drzazga on 14 January 1962 and nominated vicar at the parish of the Holy Trinity in Kwidzyn shortly thereafter.

In the years 1976–1978, he accompanied the nuncio for special assignments, Archbishop Luigi Poggi, on trips to the People's Republic of Poland.

On 18 October 1978, two days after Cardinal Karol Wojtyła became Pope John Paul II, Kowalczyk was asked to set up a Polish section of the Vatican Secretariat of State.

[1] According to the daily Rzeczpospolita, documents held by the Institute of National Remembrance indicate that, from 1982 until 1990, Kowalczyk was registered by the Polish Communist secret police (Służba Bezpieczeństwa) as a source of information under codename "Cappino".

[1][4] Kowalczyk chose the words Fiat Voluntas Tua ("Thy will be done", quote from the Pater Noster) 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.

[7] 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.

[8] 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.