In 1688, the Bishop of Kraków, Jan Małachowski, allowed the Trinitarians from Lviv to settle in Kraków on land received in Kazimierz from the starost of Oświęcim, Józef Adam Lubowiecki. Construction of the church with the monastery buildings began in 1741, according to a design by Francis Placidi. Due to the lack of funds, work was stopped after two years and then resumed in 1751. The church was consecrated in 1758. After the Austrian authorities dissolved the order in 1796, the church was used as a military storehouse. In 1812, by decree of Frederick August, Duke of Warsaw, the church was taken over by the Brothers of St John of God, a hospital order founded in the 16th century in Spain by St John of God. The Brothers of St John of God still care for the sick today, running hospitals, clinics, nursing homes and pharmacies and practising herbal medicine. 

The church is single-aisle with a row of side chapels opening into the nave through slender passageways. The interior of the nave and chapels is decorated with stylistically uniform late Baroque stucco and illusionist polychromes from 1757-1758, referring to the history of the Trinitarians – the ransom of Christian captives from Turkish hands, which were created by Joseph Piltz from Moravia and the monks. Historically, all altars were polychrome. Today's pseudo-Baroque and painted main altar dates from the 1940s. It houses a painting of Saint John of God by an unknown artist from a Kraków studio, covered with silver cloths from the early 19th century.

Next to the church is a pedestrian and bicycle bridge over the Vistula – ‘Bernatka’. It is named after the monk Laetus Bernatek, who was instrumental in constructing the St John of God hospital in Kraków.