The cathedral was originally the "church of Manila" officially established in 1571 by a secular priest, Fray Juan de Vivero, who arrived in Manila Bay in 1566.[5] De Vivero, the chaplain on the galleon of San Gerónimo, was sent by the Archbishop of Mexico, Alonso de Montúfar, to establish Christianity as the spiritual and religious administration in newly colonized Philippines. De Vivero later became the vicar-general and the first ecclesiastical judge of the city of Manila.
Spanish conquistador Miguel López de Legazpi chose the location of the church and placed it under the patronage of Santa Potenciana. The first parish priest of the church was Fray Juan de Villanueva.[6]
When the church was elevated to a cathedral in 1579 (coinciding with the canonical erection of the Diocese of Manila), a new structure made from nipa, wood, and bamboo was constructed in 1581 by Domingo de Salazar, the first-ever bishop of Manila. The new structure was consecrated on December 21, 1581; formally becoming a cathedral. The structure was destroyed by fire in 1583, which started during the funeral Mass for Governor-General Gonzalo Ronquillo de Peñalosa in San Agustin Church that razed much of the city.[2] The second cathedral, which was made of stone, was built in 1592. However, it was destroyed by an earthquake in 1600.
Construction of the third cathedral began in 1614. The new structure, consisting of three naves and seven chapels, was blessed in 1614. It again toppled by another earthquake which shook Manila in 1645.
The fourth cathedral was constructed from 1654 to 1671. In 1750, a media naranja ("half orange") dome was added to the crossing by the Florentine friar Juan de Uguccioni, who also introduced a transept to the structure.[7] It was severely damaged in 1863 by a very strong earthquake, that also damaged the palace of the Governor General of the Philippines. The seventh cathedral was constructed from 1870 to 1879. It was solemnly consecrated in December 1879. The cross atop the central dome is a reference point of astronomical longitudes of the archipelago. In 1880, another earthquake toppled its bell tower, rendering the cathedral towerless until 1958.