San Agustin Church is located on General Luna Street in Manila, Metro Manila. The current structure is the third Augustinian church to be built on the site. The first San Agustin Church was built by Spaniards on the island of Luzon. It was built of bamboo and nipa and finished in 1571, but it was destroyed by fire in December 1574 during Limahong's forces' attempted invasion of Manila. In February 1583, a fire started by a candle ignited drapery on the funeral bier during services for Spanish Governor-General Gonzalo Ronquillo de Pealosa destroyed The second wooden structure built on the same site.The Augustinians decided to rebuild the church in stone and build a monastery nearby. The construction of the cathedral began in 1586, based on a design by Juan Macas. The structure was constructed with  adobe stones quarried in Rizal from Meycauayan, Binangonan, and San Mateo. Due to a lack of funds and materials, as well as a scarcity of stone artisans, the work moved slowly. The monastery was operational by 1604, and the church was formally dedicated on January 19, 1607, as the Church of St. Paul of Manila. The Augustinians officially recognized Macas, who died before the church was finished, as the edifice's builder.

The beautiful and ancient church of San Agustin, the country's oldest stone church, is made entirely of stone and was the first earthquake-proof structure to be built on Philippine soil. It is so strong, compact, and well-executed that it has withstood earthquakes, bombings, and natural and man-made disasters in its 400-year history. Its foundation is made of adobe stones sourced from the quarries of Guadalupe in present-day Makati, San Mateo in Rizal, and Meycauayan in Bulacan. It should be noted, however, that the remaining belfy, which was extended by a level in 1854, has some bricks incorporated into it.San Agustin's foundation is made of adobe stones. Winand Klassen traces the influences of church and monastery architecture to ancient western design in his book Architecture in the Philippines (1986, USC Cebu City): first, the church's two tower entrance facade likely had its roots in Syrian churches of the 6th century, such as the Basilica at Turmanin. This was later adopted by Normandy's Romanesque churches, which were later adopted by German Baroque churches and influenced the Italians. The Church of S. Atanasio dei Greci in Rome is a good example. This church bears a striking resemblance to San Agustin.