A wooden church from the 14th century burned down in 1407 and was replaced by a brick Gothic temple founded by King Lasdislaus the Short, who placed it under the care of the Kraków Academy in 1418. In the 15th century, the presbytery was extended, and Academy professor John Cantius was buried in the church, whose remains were transferred to a Renaissance tomb in 1549. In the 17th century, after the beatification of John Cantius, his veneration gained ever-greater strength, and the old church was demolished in 1689. In its place, a larger Baroque church, designed by Tylman of Gameren, was erected between 1689 and 1703, following the church of San Andrea della Valle. The Italian architect Francisco Solari also carried out construction work. 

The façade was incorporated diagonally into a narrow street ending in a fortified wall. It is a two-storey building with two towers and late-Baroque cupolas. The church was erected on a Latin cross plan with a dome, a lantern at the intersection of the transept and nave, and a ring of chapels connected by passageways. Baltazar Fontana created the rich Baroque sculptural decoration, and the wall paintings were by the brothers Charles and Innocent Monti from Italy together with Karol Dankwart. The pulpit with the angel was carved in 1727 by Antoni Frąckiewicz, and the baptismal font from the old church was cast in 1646 by Jakub Erlicher. In 1822, Poland's first classicist statue of Nicolaus Copernicus, designed by Father Sebastian Sierakowski, was erected in the church. The choir has a late Baroque organ prospectus from 1723–1724, the only organ in the city with a sound from the time of Johann Sebastian Bach. In the confessional, with an altar dating from 1695-1703 and paintings depicting scenes from the life of Saint John Cantius, there is a coffin with the saint's remains and his bust carved in marble in 1875 by Franciszek Wyspiański. 

Bishop Karol Wojtyła celebrated mass here, gave retreats, met with students, and heard the confessions of the faithful.