In 1629 the bishop of Poznań, Maciej Łubieński, placed it within the Holy Trinity parish (Parafia Świętej Trójcy na Solcu), and its buildings were completed, at the behest of the king, as part of the Birgittine Order.

During the Swedish invasion (commonly referred to as The Deluge) the church fell into ruin and subsequently burnt down, but the magistrate's resolution from 1664 ensured that the hospital had an income.

A friend of King Augustus the Strong, the governor of Chełm Rybiński was invited for the ceremonial laying of the foundation stone, who set aside 40,000 Polish złotys for the building purposes.

During this time, the Pauline brothers were said to have organised the first pilgrimage from Warsaw to the Jasna Góra monastery in Częstochowa to pray to the Virgin Mary to save them from the disease.

After the war, the monastery was briefly regained (the abbot at the time was Teodor Fortuński), however in 1819 the Tsarist administration ordered the priests to be removed from Warsaw to Częstochowa and that the church was to be administered by the German Brotherhood of St. Benno.

Successive rectors were priests of German origin including Lüdicke, Amman, Gelderland, and Ballach.