The present structure is actually the third Augustinian church erected on the site. The first San Agustin Church was the first religious structure constructed by the Spaniards on the island of Luzon. Made of bamboo and nipa, it was completed in 1571, but destroyed by fire in December, 1574 during the attempted invasion of Manila by the forces of Limahong. A second church made of wood was constructed on the site. This was destroyed in February 1583, in a fire that started when a candle set ablaze the drapes of the funeral bier during the interment of the Spanish Governor-GeneralGonzalo Ronquillo de Peñalosa.
The Augustinians decided to rebuild the church using stone, and to construct an adjacent monastery. Construction began in 1586, based on a design by Juan Macías. The structure was built using hewn adobe stones quarried from Meycauayan, Binangonan and San Mateo, Rizal. The work proceeded slowly due to the lack of funds and materials, as well as the relative scarcity of stone artisans. The monastery was operational by 1604, and the church was formally declared complete on January 19, 1607, and named St. Paul of Manila. Macías, who had died before the completion of the church, was officially acknowledged by the Augustinians as the builder of the edifice.
San Agustin Church was looted by the British forces which occupied Manila in 1762 during the Seven Years' War. In 1854, the church was renovated under the supervision of architect Luciano Oliver. Nine years later, on June 3, 1863, the strongest earthquake at that time, hit Manila leaving widespread destruction to the city with San Agustin Church, the only public building left undamaged in the city. A series of strong earthquakes struck Manila again on 18–20 July 1880. This time, the tremors left a huge crack on the left bell tower of the church The crack was eventually repaired, but the left tower was permanently removed as it appears today. The church withstood the other major earthquakes that struck Manila before in 1645, 1699, 1754, 1796, 1825 and 1852.
On August 18, 1898, the church was the site where Spanish Governor-General Fermin Jaudenes prepared the terms for the surrender of Manila to the United States of America following the Spanish-American War.
During the Japanese occupation of the Philippines during World War II, San Agustin Church was turned into a concentration camp for prisoners. In the final days of the Battle of Manila, hundreds of Intramuros residents and clergy were held hostage in the church by Japanese soldiers; many of the hostages would be killed during the three-week long battle. The church itself survived the flattening of Intramuros by American forces in May, 1945 with only its roof damaged, the only one of the seven churches in the walled city to remain standing. The adjacent monastery however was totally destroyed, and was later rebuilt in the 1970s as a museum under the design of architect Angel Nakpil. The church was renovated in 2013, replacing its colorful facade with a mature stone-colored one.
The San Agustin Church is patterned after some of the magnificent temples built by the Augustinians in Mexico, its present edifice was built in 1587, and completed, together with the monastery, in 1604.The atmosphere is medieval since “both church and monastery symbolize the majesty and equilibrium of a Spanish golden era.”
The massive structure of the church, the symmetry and splendor of the interiors (painted by two Italians who succeeded in producing trompe l'oeil), the profile of the mouldings, rosettes and sunken panels which appear as three-dimensional carvings, a baroque pulpit with the native pineapple as a motif, the grand pipe organ, the antechoir with a 16th-century crucifix, the choir seats carved in molave with ivory inlays of the 17th century and the set of 16 huge and beautiful chandeliers from Paris.