In his neighborhood was a hospital and a poorhouse. After the Reformation, the hospital church became the evangelical church of the Slovak population of Prešov. After the order of King Leopold I, in 1673 the church was handed over to the order of minorities who came to Prešov in the same year. In addition to the church, the Minorites also owned a hospital - a hospital. In the 17th century. it was connected with the Minorite monastery and in the 18th century it was rebuilt in the Baroque style into its current form.
In 1757, four larger frescoes from the life of St. John the Baptist. To this day, they are preserved on the ceiling of the nave. The church belonged from 1818 to the Greek Catholic Diocese. In the northern chapel there is a sarcophagus in front of the altar with the remains of Bishop Petr Pavel Gojdič. His remains were placed in the sarcophagus after his beatification in 2001. On the north wall of the cathedral is a glass of a Turin canvas, which the Prešov cathedral received as a gift from the Archbishopric of Turin in Italy in 2003. .
In the 1950s, the church was put into use by the Orthodox Church, when the Greek Catholic Church was abolished in Czechoslovakia. He returned to her in 1968, after the restoration of the Greek Catholic Church. Undoubtedly the most important event in the history of the Cathedral of St. John the Baptist and the Bishop's Palace, as well as the whole diocese was the visit of Pope John Paul II. on July 2, 1995, when he was on an official visit to the Slovak Republic from June 30 to July 3, 1995.