The grotto had become a popular pilgrimage site by the early 17th century, and in 1610 it was entrusted to the Spanish hermit Juan Benegas de Cordoba.

The underground level is linked to St. Paul's Grotto, and it also contains a number of Punic, Roman and Early Christian hypogea which are interconnected with a complex of World War II-era air raid shelters.

[1] The building which houses the museum is scheduled as a Grade 1 national monument by the Malta Environment and Planning Authority.

[4] An art gallery is found on the museum's main floor, and it contains paintings by a number of artists including Mattia Preti, Antoine de Favray and Francesco Zahra.

The collections also include several sculptures, an altar which was used to celebrate Mass on Hospitaller galleys, antique silverware, relics, pottery, coins, maps, rare books and prints.