The baroque church was built in stages between 1679-1733, designed by Jan Ceroni and Jakub Fontana. There is a building next to the monastery from 1727.
In the 19th and 20th centuries, the monastery went through the very difficult times. A prison and an orphanage were located here, as was the Warsaw Academy of the Priesthood. After the Warsaw Uprising, Germans shot civilians in the church courtyard, and in 1944 the church was bombed, but not burnt, so many elements of the original Baroque architecture survived, including the pulpit (which was reconstructed using preserved fragments), side altars, epitaphs, organs and paintings from the 17th and 19th centuries. In the church the relics of St. Vitalis are kept in a glass coffin, donated to the Franciscans by Pope Benedict XIV in 1754.