The building was subject to various alterations during its history, including of which extensive reconstruction of the façade to integrate shops at ground floor level during the early seventeenth century.

Of particular importance are the Red Skorba figurines, the earliest local representations of the human figure and the predecessors of the statues of later temple periods.

Rock-cut tombs reached their climax in burials like the Ħal Saflieni Hypogeum and the Xagħra Stone Circle;[3] photographs of both sites are displayed in the museum.

[1] These rooms show examples of architecture, human representation and other items that date from the Mġarr, Ġgantija, Saflieni and Tarxien phases of Maltese prehistory.

The museum exhibits numerous corpulent statues representing human bodies unearthed from temple excavations, along with phallic representations.

The discovery of temple altars and corpulent human representations suggests that some type of cult existed on the islands of Malta and Gozo in prehistory.

The richly decorated temples which defined the previous culture, are replaced by fortified settlements, built into rocky natural defences, that bear witness to more defensive newcomers.

Body ornaments made of fish-bones, shell and faience, as well as daggers and axes, discovered in Bronze Age burial sites, accompanied the cremated remains.

The model and accompanying video by the late and renowned Dr. David Trump shows features such as depth, slope, lurches and forkings which give a sense of their configuration in the Maltese landscape, and delves into a number of possibilities.

Stemming from a donation bequeathed by Prof. Salvatore Luigi Pisani (1828–1908) in 1899, the collection has continued to grow and now consists of more than 16,000 coins, commemorative medals and dies.

The collection boasts coins from each occupation including, Punic, Roman, Byzantine, Muslim, Norman, Aragonese, the Order of St John and British.

The museum plans to open the first floor galleries and expand the exhibition in the near future to include archaeological artifacts from the Roman and Medieval Periods.