The parish of Naxxar is one of the 10 parishes mentioned by Bishop de Mello in 1436. The present parish church which is dedicated to the Nativity of the Virgin Mary was built in the early to mid-17th century due to an increasing population.

The original design has been attributed to architect Tumas Dingli. The plan of the church is based on a Latin cross conforming to the architectural trend of church building in Malta at the beginning of the 17th century. The original façade of the church followed the typical wide column structure and was divided into three vertical bays. At the beginning of the 20th century work began on the foundations for a new façade with high steeples and side chapels. The original design and proportions of the church had been heavily changed due to these alterations and enlargement.