He continued to nurse locals and sailors from this location for over 20 years before running into debt, as a result of which he transferred the hospital to the "Orden de San Juan de Dios" (Spanish: Order of Saint John of God).

Much of the building fell into ruins after it was severely damaged by Franco-Spanish bombardment during the Great Siege of Gibraltar, and it was not until 1815 that it was extensively rebuilt under the auspices of the then Governor of Gibraltar Sir George Don, as a civil hospital for the local population.

In 2005 St Bernard's Hospital moved to its new home in Europort, and over four centuries of history came to an end.

Work on the project commenced on 8 July 2002 involving radically altering the inner areas of the existing Buildings 1–4, to adapt them to the needs of a modern hospital.

The hospital is designed for some 210 beds covering ortho trauma, maternity, surgical, medical and paediatric wards, two main operating theatres and an emergency back up theatre, a hydrotherapy pool with a full rehabilitation clinic, day surgery unit and cardiac rehabilitation, accident and emergency department with provision for major and minor incidents and ophthalmic clinics.