There are a lot of debates about the early beginnings of Our Lady of Mellieħa. The devotion to this painting increased a lot during the centuries and this resulted in the building of a sanctuary dedicated to Our Lady of Mellieħa.

According to a very old tradition the highly venerated Marian Sanctuary of our Lady of Mellieħa goes back to St. Paul’s shipwreck in the 1 st century AD. The tradition says that the sanctuary was blessed by St. Paul the Apostle after he had landed in Malta. Apart from this, the tradition continues that the icon of our Lady painted on the bare rock is the work of St. Luke the Evangelist. This theory is strengthened by later important persons like Mons Pirri (1630), Gian Frangisk Abela, Giacomo Bosio, Count G.A. Ciantar and Mons O. Bres.1

Meanwhile, a number of experts of the Marian iconography attribute this style of painting to the early beginnings of Constantinople.2 On the other hand, Mario Buhagiar says that although this is one of the earliest surviving icon of the Virgin painted on the rock, it is Byzantine in inspiration but Sicilian or Southern Italian in execution. The icon is stylistically datable to the late 13 th or early 14 th centuries and it displays a close iconographic similarity with several apparently coeval murals of the Madonna in the rock-cut churches of eastern Sicily.

There are two legends telling about a consecration that happened in the early Medieval Period. This is mainly attributed to the fact that there is a painting in the sanctuary ceiling showing a number of bishops. It is believed that they represent twelve bishops who according to a pious legend visited the cave sanctuary while on their way to a Council at Milevo, near Carthage in 416. Seven crosses painted on the walls are claimed, on no evidence, to indicate that these twelve bishops consecrated the cave.4 Another legend says that this cave-church was consecrated by a number of Byzantine bishops, after they had landed in Mellieħa Bay with general Belizarius. It is important to say here that Belizarius was that Byzantine general who was sent by Emperor Justinian to reconquer the lost western provinces of the Roman Empire. These western Roman provinces were captured by a number of German Barbarian tribes.

On 30 October 1729 the French Bishop of Malta Alhperan de Bussan, visited the sanctuary too. He wanted that if someone was to visit Mellieħa, he would find some commodity, after he had travelled a lot to arrive in the village. When he arrived at the entrance of the church, the Bishop was welcomed by Fr. Domenic Farrugia, the rector of the sanctuary.After he had visited the church he went on his horse to the Port of Mellieħa Bay, where a galley was waiting for him, and continued his trip to the Grand harbour.

Bishop de Bussan strived to enlarge the church and he asked Michael Micallef to prepare a plan for the enlargement of the sanctuary. In early 1744 Fr. Domenic Farrugia got to know that on the 28 May of the same year there was to be a pastoral visit by the Bishop of Malta. The procurators of the Church wanted to consecrate the sanctuary during his visit. So, the procurators Fr. Alwig Gauci and Fr. Vincent Galea wrote a statement to the Bishop, telling him about the history of the sanctuary. Bishop Alpheran was in favour of that consecration. It was not done in that year, but three years later in 1747, when he returned to Malta. The sanctuary was consecrated on 22 may 1747. The ceremony of the consecrated took five hours to complete. From this period onwards the donations to the sanctuary continued to increased, which included paintings and other items. After the Hospitallers were forced to leave the Island by the French, the latter were too forced to surrender by the Maltese insurgents with the help of the British navy and army. The early colonial period of Malta saw no changes for the Sanctuary of our Lady of Mellieħa. In 1827, Philip Laferla re- painted the painting of the bishops. At this period the sanctuary was enlarged for another time.

On 1840, the Bishop of Malta, Francesco Saverio Caruana, wrote to Pope Gregory XVI to ask him to declare Mellieħa as a parish church because the population of Mellieħa was increasing. We have to bear in mind that at this time Mellieħa was again forming part of Naxxar parish church. The first parish priest of Mellieħa of this period was Fr. Paul Le Brun. The sanctuary continued to be enlarged.

 
When Fr. Le Brun resigned, Fr. Joseph Baldacchino was appointed as the second parish priest of the village. During his period a titular statue of Our Lady of Victory was made by sculptor Pietro Paolo Azzopardi and it was finished on 6 September 1853. Another statue is that of our Lady of Rosary, which was made in 1859. A clock was made by the British Governor on the sanctuary. Fr. Baldacchino died on 31 December 1879.