Built from 1602 to 1640[1] by the Jesuits, during the time in which Portugal and Spain were under the same crown, the church was one of the largest Catholic churches in Asia at the time. It was destroyed by a fire during a typhoon on 26 January 1835.[1] The Fortaleza do Monte overlooks the ruin.

 Virgin Mary stepping on a seven-headed hydra.

The ruins now consist of the stone frontispiece.[2]: 121 The façade sits on a small hill, with 68 stone steps leading up to it.

The façade is shaped like a retable and themed around the Assumption of Mary.[2]: 122  Likely influenced by Japanese Christian craftsmen who worked on it, the ruins of St. Paul's include carvings with heterodox images that draw from Asian traditions, including Mary stepping on a seven-headed hydra, described in accompanying Chinese characters as "Holy Mother tramples the heads of the dragon".[2]: 122  The base of the structure has six Chinese guardian lions carved from stone.[2]: 122 

The Japanese Christian craftsmen who worked on St. Paul's were converted by Jesuits and expelled from Japan in 1587 when Toyotomi Hideyoshi banned Christianity.[2]: 122 

The remains of around 250 Korean and Japanese slaves from the Portuguese slave trade are buried near the church.[3]