The first small church dedicated to St Margaret the Virgin and Martyr in Bormla existed before the year 1622. At the beginning of the 18th century, it was demolished to make room for the construction of the Santa Margherita Lines.

As compensation, the Knights gave 400 scudi and a piece of land so that the church and monastery of St Margaret could be rebuilt. The contract for the building of the new church was made on 21 July 1719 and the builder was Anton Azzopardi from Ħal-Luqa. The building of the church was completed around 1720 and it was consecrated by Bishop Vincenzo Labini on 28 October 1787.