From very early times, the sanctuary became a place of pilgrimage where many people came to pray to Our Lady for help, both spiritual and temporal, as is witnessed by the many votive offerings housed in the sacristy  of the sanctuary.  Pilgrims came from all walks of life, some of the most humble origins and others from the higher classes, including members of the Maltese nobility, Knights of Malta, some of whom were regular visitors, and also foreigners amongst whom the Viceroy of Sicily. Indeed, Grand Master Manuel Pinto de  Fonseca was such a frequent visitor that he commissioned a room to be dug at the back of the sacristy so that he could rest there.

The Pilgrims’ Lodge in fact served this purpose, as a resting place for people coming to visit the sanctuary, a strenuous journey in days when travelling was difficult. The Lodge consists of two storeys each having nine rooms. The lower storey, built towards the end of the 16th century, faces Marfa Road and its back is the side of the hill on which the sanctuary is built. This storey is the oldest still standing building in Mellieha. The upper storey was added, in stages, in the early and middle 18th century, at the same time that the sanctuary itself was built. They face the sanctuary yard and their back is on Marfa Road.

While, originally, the Pilgrims’ Lodge hosted pilgrims visiting the sanctuary, it later passed through various other uses. It later  degenerated into being used as simple store rooms. During the last century, it served for a long time as a place where catechism classes were held for the local children.