Between 1596 and 1610 local mariners contributed towards the erection of a convent and a church dedicated to Our Lady of the Visitations probably also known as Our Lady of Porto Salvo (Save Haven) because of its position overlooking the Grand Harbour. The Community (Oratory) of St Philip Neri, established in 1662, adopted this convent as their cloister – rebuilding it in 1744. The convent passed onto the Jesuit Community in 1781 but was taken over by the British Governor Sir Henry Bouverie in 1837 when it served as a hospital for victims of the first cholera epidemic.

The church’s developments followed the Oratory’s fate: it was enlarged in 1684 and again in 1741, consecrated in 1781, and sheltered the Basilica’s treasures when the Basilica was destroyed in 1941. Until it was rebuilt, the church also served as the Parish Quarters.