During and after World War II, Fleur-de-Lys was one of several settlements in Malta which grew significantly as refugees from the bombed-out Cottonera moved to the area.

[1] Parish priest Alfons Zammit began to search for a plot of land in Fleur-de-Lys on which to build a church for that area, and a construction site in which works had halted due to the war was chosen.

The first stone was laid down by Peter Dimech, the Prior Provincial, on 14 January 1945, and construction progressed rapidly.

The building was blessed on 31 December 1946 and it was officially opened on 1 January 1947; the main altar was consecrated by Archbishop Mikiel Gonzi on 14 May 1948.

[2][3] The church's altarpiece is a painting by Anthony Caruana which depicts the Virgin Mary giving a scapular to St Simon Stock.