At the end of the 16th century, the Court of the Holy Office obtained a much bigger site, the Chiaramonte Palace, and started a series of expansion and transformation works,  starting with the construction of new prisons and the entrance door from Piazza Marina, will configure a real citadel.

The building, built on two floors, was realized in a simple and severe way as to underline the dark caharacter to which these rooms were intended.

During the renovation works made in the first years of the 20th century, the historian Giuseppe Pitrè managed to save from total destruction the graffiti left by the prisoners of the Inquisition in some prison cells. He brought them to light himself, by working with a chisel. Under many layers of plaster, the Palermitan historian decoded figures, drawings, inscriptions and verses. A delicate work of rediscovery, has brought to light from those dark, cold and humid cells, some paintings and signs full of suffering with writings in Italian, in dialect, in Latin and even in English, giving back voice and name to who has been too long forgotten.

The restoration project, started in 2002 and totally redacted by the University's technicians, gave back to the rooms their original spatiality, freeing them from many additions that during the centuries altered their identity.

A campaign of archaeological excavation, conducted between 2003 and 2008, in the foundation of the 17th century building, has permitted to bring to light the remains of a semi hypogeum room, covered by a vaulted roof with ribs. It is assumed from the same period of the construction of the Chiaramonte Palace, and can be visited through the ancient staircase, largely recovered.

The rest of an establishment for the production of terracotta and glass artefacts from the Norman period, have been found during the same campaign. Characteristic is the presence of five circular furnaces and a squared cooling tank.