The first director of the Tunisian Antiquities Service (1885-95), René du Coudray de la Blanchère, and his immediate superior at the French ministry of Public Instruction and Fine Arts, Xavier Charmes, were the main actors of the implementation of the national Tunisian museum project. The project was conceived by Kheireddine Pacha and advisors from the French scientific body who were in an archaeological mission in Tunisia.

Only two departments were opened to the public in 1888. They were situated on the first floor of Mhammed Bey’s palace and were accessible through the big staircase starting at entrance hall or driba.  These departments were composed of:

• A covered patio where a collection of Latin inscriptions was exposed. It included the famous set of neo-Punic votive steles from Maghraoua which was owned by Mhammed Khaznadar. This space was given the name ‘epigraphic museum’ following the museographic nomenclature of that time
• A reception hall surmounted by a dome in gilded wood where mosaics, ceramics, and statuary works were exposed. This space was named ‘The Ancient Museum’. The dimensions of this hall (130 m2) allowed the mosaicists’ workshop which was created towards 1885 at the Alaoui Museum to lay the famous mosaic called Neptune’s Triumph with its Nereides and Tritons cortege on its ground.

In 1896, Paul Gauckler, an archaeologist who lives in the Medina of Tunis and who is attracted by the orientalist world, was named head of the Directorate of Antiquities and Arts. He defines the Alaoui Museum as the main place for the conservation and the exhibition of objects coming from the different archaeological excavations undertaken on the Tunisian soil.
His redistribution of the palace halls is going on with the adjunction of:

• The old dining room, renamed ‘Uthina’s Hall’, which is reserved to ground mosaics, statuary works and objects discovered during the excavations in Oudhna.
• The actual Carthage Hall with its mezzanine. The room size also allowed the insertion, on its ground, of two big mosaics illustrating the secret of vinification being delivered by Dionysos to King Ikarios and other illustrating rural life. The presentation of these works is in a highly faithful accordance with that of the whole site. It allows for a bird’s eye view from the second floor gallery.

Paul Gauckler reorganised the permanent exposition of the museum according to chronological criteria and that of objects according to category criteria. Thus, the first floor apartments of the palace and the outbuildings of the ground floor are rearranged to accommodate:

• The Christian department, the actual Thugga (Dougga) Hall, which was inaugurated in 1903 and which displays exceptional jewels and works.
• An Arab-Muslim museum in the ‘Small Palace’ and the so-called naksha hadida apprenticeship workshop for stucco work which was established in the old pavilion of the internal garden for the benefit of young Tunisian craftsmen.

Paul Gauckler took in charge especially the inventory of the Bardo collections. He is the co-author, with René Coudray de la Blanchère, of the Alaoui Museum Catalogue (the irreplaceable A.M.C.). The supplements to this catalogue were published by his successor heads of the Directorate of Tunisian Antiquities and Arts.

From 1905 to 1920, the new head of the directorate of antiquities, Alfred Merlin, reorganized the museum into halls bearing the names of great Tunisian archaeological sites. Thus, the halls of Althiburos, Carthage, Dougga, Sousse, Thuburbo Majus, and Thysdrus (El Jem) were created one by one.

Virgil’s Hall, which occupied the bedroom of the old harem, accommodated the famous mosaic representing the poet of Latinity who wrote the ‘Aeneid’ which was discovered in a house in Sousse. This new nomenclature of halls which calls for a visit of the sites is still used today.

In 1913, two events livened the Alaoui Museum halls. The first was the inauguration of an Arabic department in the private apartments of the Tunisian palace where an exhibition presented ethnographic collections and Tunisian craft products. The second event was the creation of another department reserved for the collections coming from the Mahdia underwater excavations that were conducted by Alfred Merlin between 1907 and 1911.

Thus, a decree in 1907 transformed the Alaoui Museum into a public institution with a legal personality. This text, which defines the prerogatives of the museum and designates its ordinary, extraordinary, and special resources, granted it an autonomy status. The director of the Antiquities and Arts Service had the ultimate responsibility for the museum. He was assisted by an administrative curator. Bertrand Pradère, who had already been in this position since the inauguration of the museum, assumed this role until his retirement in 1928.

In the beginning of the XXth Century, an association of the friends of the Alaoui Museum was created. It was very active until the beginning of the 1950s: it brought Europeans and Tunisians together, financially supported the museum to buy antiquities, and incited collectors to donate. The association was the vehicle of a positive image of the museum both in Tunisia and the throughout world.

The inter-war period was marked by the passage of Louis Poinssot as head of the Alaoui Museum. During the 1930s, a new wing was arranged on the first floor to accommodate a collection of mosaics (particularly marine-themed mosaics) and the mausoleum coming from the Officiales cemetery in Carthage (cemetery for the imperial administration personnel whose one of the tomb is displayed at the museum). The mosaics Hall of Ulysses and the winning horses date back to this very period. Louis Poinssot reorganized the Christian department in 1932 by laying new mosaics on its ground. He created an Islamic department in the pillared hall on the ground floor with the exposition of a funerary epigraphic collection. He deployed a museographic arrangement in the great Iwan hall of the Tunisian palace while Jewish antiquities were highlighted in the so-called Judaica adjoining hall.