The Franciscans opened their first friary in Malta in Rabat, having arrived on the islands in 1492. The church was built some years later in 1500. The first hospitalier Grand Master in Malta, Philippe Villiers de L’Isle-Adam, had a room in the friary, and he died there in 1534. The room still exists and it has been restored. The church was enlarged in 1757 with the help of contributions from Italy, Spain and Portugal. It was dedicated on 31 October 1790.
Parts of the church and convent were restored in 2003.