It was originally built in 1619 by Fra Giorgio Nibbia, a knight of the Order of St. John, and it was located near a cemetery where deceased patients from the nearby Sacra Infermeria were buried.

In 1852 its crypt was decorated with skeletal human remains taken from the adjacent cemetery, giving rise to the name Chapel of Bones (Maltese: Il-Kappella tal-Għadam).

[1] The chapel was dedicated to Our Lady of Mercy (or the Madonna della Pietà),[2] and it stood next to a cemetery where patients who had died at the Sacra Infermeria were buried.

[4][6] Over the years, local tradition held that the bones in the crypt did not belong to Sacra Infermeria patients, but to soldiers who had died during the Great Siege of Malta in 1565.

[1][8] The ruins were given a facelift by the Archaeological Services Cooperative and the Grupp Arkeologiku Malti (Maltese Archeology Group) in 2002,[9] but they have since fallen into a state of disrepair.

The upper section had a central arched window between small clusters of pilasters and running scrolls, and it was separated from the lower half of the structure by a thin cornice.

Skeletal remains of patients who had died at the Sacra Infermeria were arranged in decorative patterns on the walls, and the crypt therefore became popularly known as the Chapel of Bones.