The museum of Our Lady of Bonaria is housed in the premises adjoining the shrine, headquarters of the Order of the Mercedari.
Thanks to the presence of the shrine, the valuable museum collection was formed, as this houses the gifts offered by the faithful to Our Lady of Bonaria, mainly ex votos.
In the first room are collected the archaeological evidence of the Bonaria hill.
In the corridor on the cloister are votive paintings mainly of a seafaring theme, dating from the 18th-19th centuries, and ex votos donated by faithful who escaped slavery or shipwreck.
The second room displays the oldest and most valuable naval models in the shrine (there are currently about 150 of them).
They constitute an important anthology of the history of naval art, from the age of galleys to that of the introduction of steam and the innovations adopted by more modern ships.
The model ships on display in the museum are almost all of fine craftsmanship.
Also visible in this same room are the mummified bodies of some members of the noble Alagon family, who died of the plague in 1605 and were buried adjacent to the shrine.
Finally, we find the silver anchor offered by Queen Margaret in 1899 and the shrine treasury and precious sacred furnishings offered by sovereigns.