The cathedral was founded in the 12th century, and according to tradition it stands on the site where Roman governor Publius met St. Paul following his shipwreck on Malta.

The original cathedral was severely damaged in the 1693 Sicily earthquake, so it was dismantled and rebuilt in the Baroque style to a design of the Maltese architect Lorenzo Gafà between 1696 and 1705.

The cathedral is the seat of the Roman Catholic Archdiocese of Malta, and since the 19th century this function has been shared with St. John's Co-Cathedral in Valletta.

According to tradition, the site of the Mdina cathedral was originally occupied by a palace belonging to Saint Publius, the Roman governor of Melite who greeted Paul the Apostle after he was shipwrecked in Malta.

[1] Though there are remains of a Roman domus in the present crypt, and the tradition is a commonly believed legend, the version of event is not supported by archaeologists or historians.

[2] The first cathedral which stood on the site is said to have been dedicated to the Blessed Virgin Mary, but it fell into disrepair during the Arab period[3] (the churches in Melite were looted after the Aghlabid invasion in 870).

[3] In 1679, Bishop Miguel Jerónimo de Molina and the cathedral chapter decided to replace the medieval choir with one built in the Baroque style, and the architect Lorenzo Gafà was appointed to design and oversee the construction.

The central bay is set forward, and it contains the main doorway, which is surmounted by the coats of arms of the city of Mdina, Grand Master Ramon Perellos y Roccaful and Bishop Davide Cocco Palmieri, all of which were sculpted by Giuseppe Darmanin.

These include a late Gothic–early Renaissance baptismal font dating back to 1495,[8] the old cathedral's main door which was made in 1530, some 15th-century choir stalls, as well as a number of paintings.

Sculptors and other artists whose work decorates the cathedral include Giuseppe Valenti, Claudio Durante, Alessandro Algardi and Vincent Apap.

In 1969, the museum was transferred into the former Seminary in Archbishop's Square (Maltese: Pjazza tal-Arċisqof or Misraħ l-Arċisqof) facing the cathedral's side entrance.