The fortress was declared a World Heritage Site by UNESCO in 1997, cited as the best preserved and most complete example of Spanish-American military architecture.

A larger fort was designed in the early 1600s by Battista Antonelli (also known as Juan Battista Antonelli), a member of a Milanese family of military engineers, on behalf of the governor of the city, Pedro de la Roca de Borja, as a defense against raiding pirates.

Supplies would be delivered by sea and then stored in the large warehouse, which was cut directly into the rock, or transported up to the top level which housed the citadel.

[2] After they departed, the Spanish government ordered the reconstruction of the damaged part of the fortress and raised the garrison to 300 men.

From 1738–1740 further work was undertaken by the engineer Antonio de Arredondo, who enlarged the citadel and completed some of the unfinished platforms, with Juan Martín Cermeño and Francisco Calderín making the final changes to the structure after it was again damaged by earthquakes between 1757 and 1766.