After the Catalan conquest in the 13th century, the Christians’ objective was to establish a church dedicated to Saint Mary, and some historians believe that they provisionally used a mosque as a religious space. Construction of the new church began on the rock in the 14th century and coincides with the present-day apse of the cathedral which, like the belltower, still has its original Gothic appearance. By the 16th century it had five chapels and construction of the nave was completed.

It became a cathedral in the late 18th century, when the episcopal seat of Ibiza was established. At that time the presbytery was extended and the central choir transferred to the area behind the main altar. Today, it contains some valuable religious heritage, like the 16th-century altarpiece of Sant Gregori i les Ànimes (Saint Gregory and the Souls).