The earthquake of 1693 that ravaged the Val di Noto region in Sicily was also experienced in Malta although the damage suffered was not as extensive. However, one of the notable buildings that was partially destroyed was the old mediaeval cathedral in Mdina of which there were already plans to alter. In 1679, before the earthquake, Lorenzo Gafa was commissioned to design and supervise the construction of a new choir to the old cathedral and works were completed in the early 1680s. In 1692, some months before disaster struck, Gafa displayed plans and a model for a new cathedral which were studied and unanimously approved by the Cathedral Chapter. The earthquake only provided a greater sense of urgency to commence works to realise the vision of a new cathedral and a palace for the bishop.
The façade of the new cathedral, the one which stands to this very day, has relatively squat proportions with the width being approximately equal to the height of the twin towers with superimposed composite pilaster pairs to divide the facade into three bays.
One of the main design features of the cathedral is the dome, an imposing presence in the Mdina cultural landscape that towers above the surrounding historic urban environment.
The Malta Environment and Planning Authority originally scheduled the parish church as a Grade 1 monument on April 20, 2001 as per Government Notice 348.