Lija became a parish on February 6, 1594 and 100 years later construction on the present parish church commenced. With works completed in 1710, the church was dedicated by Bishop Labini on July 25, 1782.

The parish church of the Transfiguration was designed by Giovanni Barbara, not formally an architect but a well-respected master mason who was also responsible for the construction of the church. Around this time he was also appointed by the Order to serve on the commission reporting on the damage caused by the 1693 earthquake to buildings around Malta. It is said that Barbara’s design was influenced by the works of Lorenzo Gafà.

The façade of the church contains giant order flat pilasters raised on high plinths that subdivide it into three bays with the central bay comprising of the main entrance and a large rectangular window opening on the upper level. The plan of the church is laid on the Latin cross with a three-bay nave without side aisles and with shallow side chapels that are set within the wall thickness.

The Malta Environment and Planning Authority scheduled the parish church as a Grade 1 monument on August 26 as per Government Notice 782.