The first church of nipa and bamboo in   1571 was  officially known as the Church and Convent of  Saint Paul. This was destroyed during the Limahong invasion in 1574. Rebuilt a year later, it became the venue of the First Diocesan Synod in 1581.  Destroyed by another fire in 1586, the next church  was built in stone. This was designed by Juan Macias and was built from from 1587 to 1604. The sructure was so stable that the periodic earthquakes wrought minimal damage. One of the San Agustin's bell towers, however, collapsed in the 1863 earthquake.

It was in the vestry of the church that the Spaniards and Americans discussed the terms of surrender of the city in 1898. During the last days of the Battle of Manila in 1945, hundreds of Intramuros residents were gathered and held hostage in the church by Japanese soldiers. The priests were locked up in the monastery. Some of them were later killed in the air raid shelter massacre at the Palacio del Gobernador.

Although the convent was burned during the shelling of the city, the church survived. Repaired after the war, the church became the site of the first Philippine Plenary Council in 1953. It has remained a symbol of the glorious past in the old city of Intramuros.

An intricately carved door opens the church. Of great interest are the baroque pulpit, molave choir stalls and an 18th century pipe organ. Also found here is the tomb of Manila's founder and first governor-general Miguel Lopez de Legazpi, as well as the remains of other Spanish conquistadors. The monastery, on the other hand, houses an impressive collection of paintings, statues and church objects dating back to the Spanish period.