The medieval Matrice consisted of a single nave without aisles or transepts. The initiative for its enlargement was taken by the noble families of Gozo. Needing a decent place for their burial, they bought property adjoining the Matrice, raised a chantry on the site, and annexed it to the church.
The first chantry, a chapel endowed for the saying of masses for the soul of the testator and others buried within, was added late in the fifteenth century and the initiative came from a lady. On 21 August 1494, the Noble Paula de Navarra gave instructions in her will for the building of the first chantry. On 10 March 1501, the Noble Francia de Pontremolo similarly laid down that she was to be buried in a chapel that her heirs were to build annexed to the Matrice. From the will of the Noble Pietro Mompalao, it is known that on 19 August 1532, work was already in progress on the building of a third chantry. On 7 January 1543, still another chantry was built by Notary Giovanni Castelletti.
From these references and other sources, it is possible to draw up a plan of the medieval church. Upon entering, to the left, there was the Navarra chantry dedicated to the Virgin Mary of Loreto, a devotion that began late in the thirteenth century. Adjoining it stood the Mompalao chantry, dedicated to Saint Lucy, an early fourth century martyr from nearby Syracuse. Next to this, with a passage leading upon the presbytery, stood the Castelletti chantry dedicated to Saint Catherine of Alexandria, another early martyr of great fame. On the opposite, on the right of the presbytery, there was the Pontremolo chantry dedicated to the Annunciation of the Virgin Mary.
The high altar at the back faced due east. The Matrice was dominated by the Sancta Maria retable, a painting in tempera on wood, now in the Cathedral Museum. The vestry was on the right next to the Pontremolo chantry. The Matrice did not have a dome, but a bell tower was attached to the north-east corner.