This small church was the first to be built in Valleta by the Order of St John. Initially it was a chapel dedicated to Our Lady of Victory. the name was appropriately chosen to commemorate Malta's triumph over a Turkish invading force during the Great Siege of 1565. Works began in 1567, and traditionally it is considered to be the site where the first stone of the new city of Valletta was laid with unprecedented pomp and the unbounded joy of the population on 28 March 1566.

Our Lady of Victory church served as the first church of the Order in Valletta until 1577, when the Conventual Church of St John was completed. Grand Master La Vallette was initially buried in the former church. Upon completion of St. John's, his remains were moved to their final resting place within the Co-Cathedral.

The church underwent modifications towards the end of the seventeenth century and was remodelled once again in the mid eighteenth century.