The temple was founded by Duke Boleslaw V the Chaste in 1263, and until the beginning of the 19th century, it was associated with the monks of the Rule of St Augustine, brought from Prague and known in Kraków as the Marques. Construction of the hall–like, two-nave church with an elongated chancel began in 1295 and continued into the 14th and 15th centuries. The church burned down in 1397, was destroyed by an earthquake in 1443 and was later consumed by successive fires. Each time, the church was rebuilt. In 1617, mason Krzysztof Żelazko added the tower and porch. The body of the church was rebuilt as a three-nave church in 1621 and the presbytery was rebuilt in 1647; the tower base was also widened, and the chapels were fitted out. The church was restored after the 1724 fire. At the beginning of the 19th century, the Austrian authorities took over the church and monastery. In 1807, it was fitted out as a home for retired priests. It was repaired in 1841 and underwent further improvement between 1894 and 1896 through the efforts of the priest Wawrzyniec Centt. Part of the monastery was demolished between 1936 and 1938. In 1961, Karol Wojtyła established the Michał Giedroyć Theological Institute, saw to the care of the church and funded the altar. Another restoration was carried out between 1972 and 1974.

The church has retained its Gothic character and early Baroque furnishings. It is a three–nave basilica with a quadrilateral tower, galleries over the side aisles, and an elongated chancel closed at three sides. On the outer wall of the church is a niche with a copy of a 15th–century Gothic crucifixion group. Adjoining the nave is the Chapel of Our Lady of Częstochowa with a painting of the Madonna. The wooden main altar of 1618 comes from the workshop of the woodcarver Baltazar Kuncz. Baltazar Fontana made the statue of the Angel in the presbytery. Attention is drawn to the heart–shaped pulpit with the cross as the symbol of the order. A Gothic pointed portal leads to the Giedroycianum, a chapel and rooms dedicated to the blessed monk Michał Giedroyćć. There are reminders of the Order of Marques, a Gothic-Renaissance triptych from 1520 and the Chapel of Our Lady of Giedroyć with a painting of the Madonna from 1450–1460.