In 1575 when Mons. Royas helmed the episcopate of Malta, Mons. Duzina headed the Apostolic Visit which surveyed the Parish of Rabat. Mons Duzina found standing a very old church dedicated to St. Paul. However it was in such bad conditions that another church was being built to replace it in the whereabouts.
The ground on which the church is built on holds very sacred connotations for the people of Rabat because it is believed that it was the same ground on which St. Paul the Apostle, St. Luke the Evangelist and St. Barnaba and St. Aristarcus the disciples dwelled and preached. Chrisostomus recounts how these saintly figures baptised the locals as Divine Providence fated after the shipwreck on the island. This same ground knows the very beginning of Christianity in Malta when Salvation was preached for the first time. St. Paul spent his three month Winter stay in Malta in a grotto underneath this church. The whereabouts confine also the first Christian cemetries.
The construction of the present church started after the feast of 1653. We know this because Bishop Balaguer paid a Pastoral Visit on the 3rd June, 1653 but no mention of any construction is made in his personal journals. However Balaguer visited the church on the 18th April 1656 where he described the advanced construction of the sagristy and the tribune only. The side chapels and the dome were missing. Balaguer praised Cosmana Navarra and her husband Lorenzo Cassar for being such great benefactors.
However construction had subsided by 1662 because the Pastoral Visit made on the 5th June of that same year made no mention of any progress. Works resumed on the 19th January 1664 after the signing of the contract between Cosmana Navarra and mastermasons Lorenzo Gafa and Paoluccio Formosa in which it established that the sum of 1700 escudos were enough for the completion of the church, to dig the charnel-house and to complete the already partly built belfry. In his visit on the 7th January 1666 Balaguer describes the almost completed church as magnificent with the side chapel dedicated to St. Anthony in its advanced state.
Construction faced critical moments when works on the side chapel dedicated to St. Stephen were at a halt. The church plan allocated this side chapel beside the main altar dedicated to St. Publius which fell under the property of the Grand Master who refused to concede it. Probably the Grand Master had other plans in his mind or he was weary the new church would surpass the Order’s chapel.
Ix-xoghol li nbeda fl-1653 kien ga waqaf ghal kollox fl-1662 ghax ma jissemma xejn fil-Vista pastorali li saret fil-5 ta’ Gunju ta’ dik is-sena. Zgur li x-xoghol rega’ tkompla mid-19 ta’ Jannar 1664, kif jirrizulta mill-ftehim notarili li Cosmana ghamlet fis-16 ta’ April mal-bennejja Lorenzo Gafa’ u Pawluccju Farmusa ghal ispiza ta’ 1700 skud biex titkompla l-Knisja, tithaffer il-karnierja u jitkompla il-kapmnar li minnu kienet diga tlestiet parti. L-Isqof Balaguer fil-Vista tieghu tas-7 ta’ Jannar 1666 jikkummenta li l-knisja, li jsejhila ‘manjifika’, kienet prattikament lesta, bil-kappellun ta’ San Anton mibni ghal kollox. Meanwhile Cosmana Navarra embellished the church in 1678 with Erardi’s famous titular painting depicting the Shipwreck. The churchyard was ready in 1679. A year later in 1680, Cosmana Navarra rejoiced when the newly appointed Grand Master, Fra Nicola Cotoner conceded the much needed property for the construction of St. Stephen’s chapel on the same day of his election. Apart from donating part of her riches to build the façade of the church, Cosmana Navarra contributed also to the construction of the side walls leading to St. Publius’ Chapel and to the churchyard.