On 23 December 1615, the villagers made a request to Bishop Cagliares to establish Zabbar as a parish. The request was granted, and on 10 January 1615, Fr Angelo Pontremoli took possession as the first Parish Priest of Zabbar.
At that time, the vice-parish of the village was that of St James, a largish church well-frequented by the locals; but the choice of a parish fell on the small chapel dedicated to Out Lady of Graces. This was due to the intense devotion which this shrine had already attracted to it since the very days of its erection as a very small humble chapel dedicated to the Mother of Graces.
By time the chapel began its transformation. Actual reconstruction began on 1 May 1641, on a plan by the well known Maltese architect Tumas Dingli, with the then parish priest Fr Frangisk Piscopo actively set on seeing the work through. It was finished in about 1696. As time went by, the villagers requested that the façade of the church, together with other structural features, be altered. Archpriest Ganni Bonavia came into the picture. Bonavia, who resided at Zabbar, designed the required plan and in 1738 work began on a new façade and the erection of two steeples. When the work was ready, in 1742, the church underwent other structural changes – the inner part of the façade, the burial vault and the marble pavement.
In 1911 the church was further enlarged by the addition of six naves, three on each side. Some time after, a clock which could chime the Ave Maria was installed in the right-hand steeple. On 2 September the present magnificent dome, depicting the Eight Beatitudes, replaced the smaller one, which due to an earth tremor and the relentless battering during the past attacks on it by the French troops, had sustained severe damage, had become dangerous and was demolished. This dome was built on a plan by Architect Gius. Pace and the construction supervised by Fr Frangisk Sciberras.
This church is built in the form of a Latin cross and is quite largish. It consists of a choir, two large side chapels, an aisle and two sacristies. It is 47 meters long and 32.4 meters wide, while the aisle is 8 meters long. It is built on the Corinth plan. During a fierce storm in 1902, a lighting bolt hit one of the steeples and demolished a part of it. Among the bells one can find in the steeples, there is the large one made in 1891 by the founder Gulju Cauchi, which cost ₤380. besides this bell, Cauchi made another two.
The Sanctuary Museum of Zabbar is one of the finest examples of its kind on Malta, contains the largest collection of maritime votive paintings of the Order of St John in Malta. Other items on display include a picture gallery, sedan chairs, a portable altar, a unique large painting of the Gran Carrack Sant Anna, former titular paintings, a medieval fresco, a complete ceremonial suit of armour, statues, silverware, stamps, documents, coins, medals, sculptured wooden fixtures from the ship R.M.S. Alcantara, the sole surviving plague hearse, the clock mechanism formerly in the Sanctuary’s belfry and the remains of an R.A.F. Vulcan Bomber which exploded over Zabbar in 1975. The museum, which was inaugurated in 1954, was refurbished in 2003.