Although Hawkins and Drake both managed to escape the organized entrapment on their respective warships, many of the trapped sailors aboard the ships were killed by Spanish cannon fire.

Trapped, and with no rescue in sight, these sailors ventured further inland, where they eventually settled among the local population and integrated into the Mexican populace at large, becoming part of the European diaspora in Mexico.

The attack by the Spaniards at San Juan de Ulúa is credited as marking Drake's first feelings of intense hatred of both Catholicism and the Spanish, which would both go on to have an influence on his later career.

The original icon has been missing for hundreds of years, its memory lost, ever since Mexico gained independence as this restricted entrance into the walled citadel and broke the Manila galleon trade linking Veracruz with Havana, Puerto Rico, Portobelo, Callao, San Blas, the shipyards of Barra de Navidad, Acapulco, the shipyards of Cavite, and eventually, Manila.

Her feast day is known for the crowds of Filipinos that come to offer thanks and to pray the rosary, as well as watch a bull run called Fiesta De Los Toros, and another one, called Parada de Los Toros, highlighting cows and water buffalo and carromatas (a type of farm buggy or cart) festooned with flowers in a colorful parade, following the blessing of the farm animals.

After Mexico's independence in 1821, a large body of Spanish troops continued to occupy San Juan de Ulúa as late as 1825.

Since then, San Juan de Ulúa has served as a military and political symbol of Mexican resistance to foreign invasions and occupations, several of which took place during the 19th century.

A portion of San Juan de Ulúa also served several times as the presidential palace, housing presidents such as Benito Juárez and Venustiano Carranza.

The prison, along with the remaining fortress complex are all open to the public, with the exception of the former presidential palace, which suffered severe decay and is still undergoing renovations as of 2020.