Building construction commenced on 25th June 1586. Blacksmiths, masons and carpenters from Pampanga, Bulacan, Batangas, Ilocos and Visayas (i.e., Provinces where the Augustinians were present in large numbers) worked on the project, along with Chinese stonecutters from the Parian.
Cartloads of wood were transported from Pampagna, and hewn stone from quarries at Guadalupe, Meycauayan and San Mateo.
For the necessary finance, various sources of income were tapped. The Provincial, Martin de Rada O.S.A., issued an appeal for funds. Not only was money accepted, but also chickens, rice, bamboo poles and rattan.
The income of bequests to the Order were used, and income derived from the estates owned by Augustinian monasteries in Pasay, Bulacan, Tondo, Malinta and Mandaluyong.
Two Augustinians, Frs Diego de Cerrabe O.S.A. and Pedro de Acre (who later became the Bishop of Cebu) were particularly successful in obtaining funds from other Augustinian monasteries throughout the Philippines.
An appeal to the King of Spain through the Royal Audienca led to a pledge via a Royal Order from the Spanish King in 1584 (i.e., after the burning of the second church). Although 10,000 ducats was pledged, only 2,000 pesos ever reached the Augustinian Prior in Intramuros.
Although funds were scare, construction was in full swing by 1591.
By 1593, when there were twenty-eight Augustinians living in the adjacent monastery, the project was well advanced. Further general appeals were made in 1597 and 1602.
The church stands on very solid ground, and measures 67 metres in length and 25 metres in width. The height inside the church to the cornice is 12 metres, and the top of the dome is 28 metres above ground level. The walls are made of hewn stone.