The painting of Our Lady of Dolours in the Franciscan Church has been surrounded with prayer and devotion for over 500 years. It is connected to a tradition of pardoning criminals sentenced to death.

The 15th-century Chapel of Our Lady of Dolours, takes up a section of the cloister. The late-Gothic painting in a newer altar of black marble dates back to around 1510. It belongs to the Mater Dolorosa type, with the Mother of God depicted in an expressive pose of prayer, with the weary face portraying a sense of anguish and sharing the suffering of Christ. The angels hold the tools of the passion of Christ (arma Christi), and the sense of anguish is emphasised by the sword piercing the heart of Mary. The 17th-century painting above is a Veraicon, i.e. representation of the face of Christ printed on the veil of St Veronica.

The icon in the Franciscan Church has been known as the Sorrowful Patron of Kraków for centuries, with a special devotion emergent in the days of the Baroque. In the 17th and 18th centuries, prisoners sentenced to death and saved from their sentence by the Archbrotherhood of the Passion of Christ operated by the monastery were given their pardon before her face.

When in 1850 the painting was (again) saved from a great fire of this quarter of the city, people recognised it as divine intervention and began to campaign for its coronation. Famous for countless miracles and graces, the painting finally received a papal crown in 1908. It is modelled on the crown of Anjou of Jadwiga Queen of Poland, today a saint. Karol Wojtyła used to pray here, and had the custom of celebrating his private Way of the Cross in the Franciscan Church. The future Pope John Paul II also frequently listened to confessions in a confessional in the Chapel of the Passion of Christ by the northern wall of the church.

The Chapel of Blessed Salomea holds the mortal remains of the blessed lady: a 13th-century Piast Princess, sister of the founder of the Franciscan Monastery, Duke Boleslaus the Modest (Bolesław Wstydliwy) and the first Polish Poor Clares nun. One of the monumental stained-glass windows in the chancel, designed in the style of Young Poland by Stanisław Wyspiański, is dedicated to Blessed Salomea.

The Altar of St Maximilian (devoted to Maximilian Maria Kolbe, a Franciscan and martyr who offered his life for a fellow inmate of KL Auschwitz in 1941) stands in the nave of the Basilica of St Francis of Assisi, and a plaque by the entrance to the monastery commemorates his pastoral service in this church in 1919–22.