Built from the foundation of the Grand Marshal of the Crown, Stanisław Herakliusz Lubomirski, the owner of Czerniaków (from 1683), it was originally planned as a family mausoleum.

Designed by the royal architect Tylman van Gameren, the Italian builder Izydor Affaita supervised the construction between 1690 and 1693.

The structure of the church has an interesting arrangement where the proportions have retained their original appearance including the interior which did not undergo major changes, keeping the decor from the end of the 17th century.

The side altars are images of St. Francis and the famous Renaissance triptych, painted on glass, the "Lamentation of Christ", which was a gift from King John III Sobieski.

At the main altar is a reliquary of the martyr St. Boniface, which Lubomirski had received from Pope Innocent XII in 1693 during a pilgrimage to Rome.