After singing in the choir of the Cathedral of Mdina, in 1738 Zerafa went to Naples. There he studied at the Conservatorio dei Poveri di Gesù under the tutelage of Feo Francesco and Girolamo Abos. He returned to Malta in 1744, where he became choirmaster of the Cathedral of Mdina. He retained that position, except for the period 1751–53, until his death.
During his period as a composer, which lasted until 1782, he wrote several sacred works (over 170), including Masses, Requiems, motets, hymns, psalms and minor sacred works. His Confitebor, composed in 1765 for soprano and instruments, is his best known piece.