During the century and a half of Turkish occupation, the vast majority of its ecclesiastical treasures were shipped to Pressburg (present day Bratislava) and following the capture of Buda in 1541 the church became the city's main mosque. Ornate frescoes that previously adorned the walls of the building were whitewashed and interior furnishings stripped out.

The church was also a place of the so called Mary-wonder. In 1686 during the siege of Buda by the Holy League a wall of the church collapsed due to cannonfire. It turned out that an old votive Madonna statue was hidden behind the wall. As the sculpture of the Virgin Mary appeared before the praying Muslims, the morale of the garrison collapsed and the city fell on the same day.