The first Gothic church was utterly destroyed during the Swedish Deluge. The current one is topped by a dome, which was deliberately placed in such a way that it did not rise abovefacade of  the church facade. The dome’s position was determined by strategic considerations – artillery fire from Wawel Castle could have damaged the over-exposed elements of the structure.
The first Bernardine friars in Kraków were recruited from among the listeners of the austere preacher, the Observant Franciscan Saint John of Capistrano, who preached fiery sermons against sin and excesses during his visit to the city in the mid-15th century. He came to Kraków in 1453, at the invitation of King Casimir Jagiellon and the Bishop of Kraków, Cardinal Zbigniew Oleśnicki, who offered the monks land in Stradom.
The construction of the first church was led by Jan Długosz and founded by Sandomierz Castellan Jan Hińcza of Rogów. Between 1645 and 1647, a new church was built on the site of the Gothic church destroyed during the Swedish Deluge. The present early Baroque church, dating from 1659–1680, was erected on a Latin cross plan according to a design by Krzysztof Mieroszewski. It is a three-nave basilica church with a transept and a dome hidden in the roof. 
There are late Renaissance tombs in the porch. The vaults of the nave and presbytery are decorated with stucco. The Chapel of Saint Anne contains a late 18th-century Baroque altarpiece with a sculpture of Saint Anne Selbdritt dating from the 15th century from the workshop of Veit Stoss, and a Baroque painting ‘Dance of Death’ from the 17th century. Meanwhile, in the Chapel of Saint Simon of Lipnica, an altar-mausoleum dating from 1662 contains a sarcophagus with the relics and statue of Saint Simon, a Bernardine friar who lived in the 15th century. The stained-glass window with scenes from the saint's life was made by Józef Mehoffer. The late Baroque side altars and the main altar with woodcarving decoration from 1758–1766 feature paintings by Franciszek Lekszycki, a monk at the local monastery.