The main crypt known as Il-Mudlama, lies precisely beneath the main aisles stretching between the main entrance to the church to just before the cancel. The crypt is all hewn in rock and roofed over by fifteen arches with stone roof slabs spanning in between. Before the construction of the side naves, the entrance to the crypt was through a flight of steps accessed from a door behind the main entrance, just behind were today there is the niche of St Catherine’s statue.
On the furthest end of the main crypt there is an altar with a stone statue of the Immaculate Conception placed in a niche, just over it. According to the historian Can Rev Joe Abela, this statue was originally placed by Fra Gabriel Cassar in the older church of St Mary located at ir-Raħal ta’ Fuq. Fra Cassar was the son of the Maltese architect Gerolimo Cassar.
The burial area right in front of this altar was reserved for the Testaferrata family the heirs of Girgor Bonici the main benefactor of this church. The first burial in this crypt dates back to 1709, with the last one taking place in 1975.
Along the north side of the main crypt, the side just beneath the nave where one finds St Michael’s altar, there are three narrow passages hewn in rock and leading to the the side facade of the church. These passages were done to facilitate air circulation within the crypt.
On the southern side, that is beneath the nave were one finds St Andrew’s altar, one finds the second crypt which was built in the mid-18th century. This crypt is roofed over with a series of cross vaults which, make it one of the local fine examples of traditional construction technology. At the end of this crypt there is a central bass relief medallion of Our Lady of the Rosary flanked on each side by soul sculptured figures. The burial area right in front of this composition is reserved for members of the clergy.
On the side walls of both crypts one can still notice marks which identify the tombs. There are also a series of holes hewn in rock which were used as candle or oil-lamp holders to illuminate the space.
It was only after the annual event of Żejt iż-Żejtun that one started appreciating these spaces, after these were opened for viewing by the general public during this event. Thanks to Paul Zammit, the sacristan of the parish church and a small number of volunteers who together have cleaned and restored these crypts and turned them into a main attraction in the historical centre of Żejtun. During main events these are lit for the occasion with candles and thus adding to the unique atmosphere of this architecturally attractive space.
The smaller crypt became an ideal space in which the Good Friday Committee every year sets up a presentation of the Last Supper with life-size figures. This presentation cannot be missed by those visiting Żejtun during the Holy Week.