The current church is built on the site of a medieval church dedicated to St Catherine with adjacent chapels dedicated to St James (St Jacob) and St Mark. Later alterations resulted in the demolition of the adjacent chapels, building of a Renaissance doorway, enlarging the footprint of the church and adding the dome.
Equidistant from the medieval villages of Bisqallin and Ħal Bisbut, the church of St Catherine served as the parish church for a cluster of small villages and hamlets in the South of the island. It is recorded in the Rollo De Mello of 1436 as the parish of Casale Sta Caterina. This church then had a rectangular shape, with a simple façade.
The old chapel’s façade, however, was turned northwards – as is a statue of St. Gregory – facing Mdina, Malta’s old capital.
Visible from the sea, by 1470, the church was recognised by sailors as a shrine. On the outer walls of the church, there are various maritime graffiti. St Catherine was the protector of sailors and those who work in lighthouses.
The church and its lands appertained to Cantor (Monsinjur tal-Virga) of the Cathedral of Mdina and coat of arms of the Cantors of the Cathedral from the 12th century (arrival of the Normans and resurgence of Christianity in Malta) are painted on the sacristy walls.
Because of its strategic location looking over the bays of St Thomas, Marsascala and Marsaxlokk, the older church doubled up as a fort/watch tower. In 1614, an Ottoman incursion in the South of Malta wreaked havoc on this church until the Ottomans were forced to withdraw to their galleys. A discovery of bones in secret passageways of the church probably date back to this black episode in the history of the island.
Following this attack the defence of the South was strengthened with further forts among them the Wignacourt towers in Marsaxlokk and Marsascala.
From the Church of St Gregory the walk loops back towards the Parish Church of St Catherine then veering first right and then left towards the Chapel of San Klement also in Zejtun.