In the Ottoman period the church was ceded to Fazil Ahmet Kiopruli and converted into the Vezir Moqsue, at which time the bell tower became a minaret. When Chandax was surrendered to the Turks in 1669, all the relics were removed to Venice. The skull of St. Titus was placed in St. Mark's; to this day, the icon of the Virgin Mary Mespoantitissa remains in Santa Maria della Salute.

The major earthquake in 1856 totally destroyed the church, which was then rebuilt from the foundations to plans by the architect Ath. Moussis.