The history of sacred music in Malta (and Gozo) dates back to the earliest times, owing its importance to a population that has always been very religious. There are more than fifty villages and towns around the islands, each of which celebrates an annual cycle of religious festivities, most of which are accompanied by processions. One can say with certainty that two ceremonial high points dominate: the first is the annual festa of the parish patron; the second is the series of celebrations that take place during Holy Week. The main centre for the performance of church music in Malta was at the Cathedral of St Paul in Mdina; archival documents provide us with enough information to enable us to situate the beginnings of the Cappella musicale towards the end of the fifteenth century.

In 1494 the first signs of organ playing are encountered, and the first organist to be engaged to serve the Mother Church was the Venerabili Frate Joannes (de) Rapi(s), who was paid an annual salary of 10 uncie. After his death in 1496 he was succeeded by Don Lorenzo Vagnolo, only to be replaced two months later by Don Nicola de Virmiglia. Two other organists are named as Fra Antonio Pericuni (1496) and Mastro Tolentio Castellano (1507). From 1515 onwards the Cathedral Chapter employed as organist Don Lorenzo Caxaro, and hired another cleric to teach plainsong, the first known being the foreigner Don Andriotta Scavuni, who was engaged to teach canto fermo (cantus firmus: plainchant, plainsong) to the clergy in the same year. In 1524 Caxaro was joined by a second organist (and organ repairer) by the name of Ximuni Ferriolu (or Feriolo), who was also a deacon. Their contract is the earliest documented reference to the renovation of the Cathedral organ.

Other music instructors followed: Don Nicola Catalano (employed in 1517) and the first two native-born Maltese educators, Don Domenico Vella and Don Andrea de Federico (employed in 1523 and 1527–8, respectively). In 1533 a certain Misser Joan Aloysi Scagluni was enrolled to teach the clerics; he was succeeded in 1535 by a Maltese Augustinian friar Padre Petro Callus, who also had the task of giving afternoon lessons in canto fermo to the choir.