Pope Urban VIII accepted Balaguer's nomination and formally appointed him to the see of Malta on February 12, 1635.

During his episcopacy Balaguer donated a wooden crucifix by Innocenzo da Petralia Soprano (1592-1648), a Franciscan friar from Sicily which today is found in the Chapel of the Holy Crucifix in St. Paul's Cathedral, Mdina.

[2] Also Bishop Balaguer consecrated the oldest bell in Malta dating from Medieval times.

The bell, christened Petronilla was, reconsecrated on August 7, 1645 and installed in its place in the cathedral's belfry.

There were numerous occasions where Bishop Balaguer was about to resign though at the same time he was needed to reform the much slacking diocese.