When the Portuguese took control of Malacca in 1511, the Sultan of Malacca escaped south and founded the Johor Sultanate, which included the island of what is today Singapore. There were records of a naval battle between Portuguese and Dutch ships off the coast of Singapore in October 1603, which the Portuguese lost. In 1613 the Portuguese destroyed the Malay settlement on the island and the place was largely forgotten until the British Sir Stamford Raffles founded modern Singapore in 1819.
By 1821, there was already a small Catholic community that included Malaccans of Portuguese descent. They were ministered by priests from the Diocese of Malacca, established in 1558, that survived the seizure of Malacca by the Protestant Dutch from the Portuguese in 1641. In turn, the Diocese of Malacca was supported by the Archdiocese of Goa and the Diocese of Macau, areas that the Portuguese continued to control.
In 1825, the Porto-born Fr. Francisco da Silva Pinto e Maia moved from Macau, where he'd spent 12 years, and founded the Portuguese Mission in Singapore. Another Catholic nation, France, was also active in Southeast Asia, and the Missions Étrangères de Paris (MEP) were carrying out missionary work in Siam (today's Thailand), Vietnam, Laos and Cambodia. In 1831 the (French) Apostolic Vicar of Siam claimed spiritual jurisdiction over Singapore, and this led to a tussle between the Portuguese and French arms of the Catholic Church that lasted over the reigns of multiple popes. The dual jurisdiction over Singapore was clarified by an 1886 Concordat between Pope Leo XII and Portuguese King Dom Luís I, stipulating that "All the Catholics in Malacca and Singapore, who are under the jurisdiction of Goa would pass to the jurisdiction of Macau".
Interestingly, the first church established in Singapore was a collaboration between the Portuguese Mission led by Fr. Maia and the French MEP. This was a chapel that opened in 1833 along Bras Basah Road, on land that would become the site of the boys' school St. Joseph's Institution (SJI) that the French De La Salle Brothers later founded in 1852. The Portuguese Mission under Fr. Vicente de Santa Catarina gained British support to build a church a few hundred metres away, and the similarly named St. Joseph's Church opened in 1853. The foundation stone, laid in December 1851, refers to the "25th year of the reign of Dona Maria II – Queen of Portugal" as well as the "14th year of the reign of Her Britannic Majesty Queen Victoria".
As Singapore's population grew, the original St. Joseph's Church became too small for the congregation and it was demolished in 1906 to make way for an expanded building. On June 30, 1912, the Manueline style (Portuguese late Gothic) church was consecrated by the Bishop of Macau, Dom João Paulino d'Azevedo e Castro.
Singapore became an independent country in 1965, and in 1972 the Archdiocese of Singapore was split out from the former Archdiocese of Malacca-Singapore. Dual jurisdiction ended in 1981 when an agreement was signed between the Archbishop of Singapore Gregory Yong and the Bishop of Macau Arquimínio Rodrigues da Costa for the transfer of the Parish of St. Joseph to the Archdiocese of Singapore. To maintain the Portuguese character of the Church, the Diocese of Macau continued to send priests to St. Joseph's Church until December 31, 1999. At that point, Fr. Benito de Sousa retired and symbolically ended the Portuguese Mission in Singapore.