During World War II, from 1941 to 1945, it served as fortification for Japanese soldiers, when the battle for liberation was fought, the fort served as an army camp . After 1950, Cebu Garden Club took over and fixed the inner court into a miniature garden. For a couple of years it also housed the Cebu City Zoo. In 1978 to August 15, 1993, it housed the offices of the Department of Tourism and the Philippine Tourism Authority. At present, it is under the care and administration of the PTA and now houses the National Museum that showcases the San Diego shipwreck & Fort San Pedro diggings.