The palace has been the seat of the bishops of Kraków since the end of the 14th century; today, it has the shape given to it in the 19th century with the preservation of Renaissance and Baroque fragments. Karol Wojtyła lived in the palace from 1964 to 1978, from his election as bishop to his election as Pope. During papal pilgrimages, he would stop at the palace and, standing in the window of the Papal Chapel, located on the first floor of the palace above the baroque entrance gate, he would informally meet with the assembled faithful. He first showed up at the window in 1979 and talked to young people late into the night. These meetings became a tradition of all subsequent papal pilgrimages. Before John Paul II's death, the faithful prayed in front of the palace, a solemn mass dedicated to the late Pope was held in the Franciscan church on 2 April 2005, flowers, mementos and candles were laid in front of the palace, and a symbolic cross was placed on the windowsill of the pope’s window. The tradition was continued by Pope Benedict XVI , who addressed the faithful from a pope’s window during his 2006 pilgrimage to Poland. In 2016, Pope Francis I also appeared in the window.

Until recently, pictures of the Pope were placed in the window. During the 40th anniversary of the election of Karol Wojtyła as Pope in 2018, a Venetian glass mosaic with an effigy of John Paul II, designed by Magdalena Czeska, was unveiled there.