The Old Prison is situated in the Citadel, overlooking Cathedral Square and adjacent to the Law Courts, to which it was originally connected. In its present form, the prison complex is divided into two sections: the entrance hall, which served as a common cell in the 19th century; and a free-standing block with six individual cells. The prison was in use from the mid-16th century until the beginning of the 20th century.
Soon after their arrival in Malta, the Knights of St John started making use of this prison by dispatching their rowdier members 'to cool down therein'. A new prison was then built in 1548. After the expulsion of the Knights of St John from Malta, the prison was not to fall into disuse. In fact, the number of inmates seems to have increased as the galleys were no longer used as a penal measure.

From the mid-19th century, another building within the Citadel started functioning as a prison and continued to serve this purpose until it closed down in 1962. At first, the new prison was in use simultaneously with the old one which, for some decades, continued to house those awaiting trial.

Today, the entrance hall houses a permanent exhibition on fortifications to be found on the Island of Gozo. The individual cells, next to a central courtyard and surrounded by a narrow corridor, are still well-preserved in their original state.

Escapes are recorded to have taken place both during the rule of the Knights of St John and British rule. Incarceration coupled with hard labour was also applied as punishment. The daily food allowance for inmates was made up of a substantial amount of bread and pasta, some cheese or salted fish and, occasionally, some olives. For water, the prison had a cistern in the corridor collecting rainwater from the overlying roofs.

The walls of the cells and corridors in the old prison are covered with graffiti. It is considered as the largest collection of historical graffiti in one single place on the Maltese Islands. The representations are often of ships, and date from different periods. There are also handprints, crosses, names, dates, games, and anthropomorphic figures etched into the limestone walls. Some inmates also appear to have scratched a tally of their length of stay behind bars. The graffiti are a fascinating, human insight into the lives of those incarcerated here.