According to tradition, the site of the church was formerly occupied by a Phoenician temple of Astarte, which was later rededicated to Juno by the Romans.

[3] It remained a private chapel for subsequent Hospitaller Grand Masters until the Order moved its base to Valletta in 1571.

[2] The chapel lost its importance at this point, but it remained in use as a church by the fort's garrison until the French occupation of Malta in 1798.

After World War II, it was converted back to a Roman Catholic chapel for the fort's Maltese workers, and it was open to the general public annually on Victory Day.

The roof is held up by a pink granite column which is of Egyptian origin and which might have formed part of an ancient temple predating the chapel.

The following Grand Masters were originally buried within this crypt,[2] but their remains were moved to Saint John's Co-Cathedral in Valletta in the late 16th century:[5]