The first small church dedicated to St Paul in the area called Maħten it-Tin in Bormla, started to be built around 1590. The building of the church seems to have been completed close to 1595.

The connection of this area with St Paul comes from the tradition which says that after spending three months in Malta, he embarked on a boat to continue his journey to Rome from this place.

In the 18th century, it was decided to build a bigger and more beautiful church in the Doric style to replace the one constructed in the 16th century. The building work was completed around 1740. The church was blessed on 22 October 1741.