Outside the eastern wall is a Marian shrine dedicated to Our Lady of the Pillar, the patroness of the city, pontifically crowned on 12 October 1960 via decree dating from 18 September 1960.

[2] In 1635, upon the requests of the Jesuit missionaries and Bishop Fray Pedro of Cebu, the Spanish governor of the Philippines Juan Cerezo de Salamanca (1633–1635) approved the building of a stone fort in defense against pirates and raiders of the sultans of Mindanao and Jolo.

Because of insufficient manpower, laborers from Cavite, Cebu, Bohol, and Panay had to be imported to help the Spaniards, Mexicans and Peruvians in the construction of the fort.

A similar but distinct narrative is described by American Captain John H. McGee, who relayed the story he heard while training soldiers at Fort Pilar, then-called Pettit Barracks.

[5] According to that version, while Dutch ships were besieging the fort, the Blessed Virgin Mary appeared to a Spanish soldier and "assured him victory if the beleaguered garrison held out."

[7] It is recounted that when another tsunami-causing earthquake struck the Moro Gulf at midnight on August 19, 1976, Mary was allegedly "once again seen over the sea, protecting people from the disaster.

"[8] Following the Spanish–American War, Fort Pilar and its Spanish troops surrendered to the Revolutionary Government of Zamboanga on May 18, 1899, under General Vicente Álvarez, a Zamboangueño, at the onset of the Philippine Revolution against Spain.