The São José met her demise grounded on a reef off the Mozambique coast, victim to final assault by the Anglo-Dutch fleet. A reported 66,000 Spanish reales were salvaged by the enemy, a small share of the total treasure aboard the ship, lost with some 300-400 passengers and crew as the vessel broke up and sank to the bottom of the Mozambique Channel.

For nearly 400 years, the wreck of the São José remained hidden off the isolated coast of East Africa until her discovery in May 2005 by Portuguese archaeology company Arqueonautas.