The church is built over the ditch of the Roman city which also included a large part of Rabat. The church is also built over the grotto where according to tradition St. Paul was kept prisoner during his three months stay in Malta in 60 A.D. In 1336 bishop Hilarius refers to the church as ecclesia Sancti Pauli de crypta , and also mentions the cemetery and the Roman ditch. Several churches have been built on the site both by the diocese and the Knights of St. John. The present church was built with funds provided by the noble woman Guzmana Navarra on plans prepared by F. Bonamico. The church was completed by Lorenzo Gafà in 1683.