The museum building, designed by the architect Aris Konstantinidis, is a modern architectural masterpiece in the city. Its geometric structure, roofs of varying heights with skylights and windows, atriums, interior and exterior canopies, windows with separate skylights, wooden frames with metal shutters, ceilings bearing the visible imprints of wooden molds, and a low wall-fence that surrounds the garden with its pine trees, contribute to its distinctive design. The Museum was inaugurated in 1976.

The exhibitions span from the Neolithic to the Byzantine period. presented in chronological order without separating the local excavation sets. The aim is to showcase selected, representative finds from the most significant archaeological sites, offering visitors a comprehensive overview of the prehistory and history of Aegean Thrace. All the exhibits highlight the significance of the Greek presence in the northern Aegean and the creative evolution of Greek art and culture in this remote northern region during antiquity. The Museum's main exhibition showcases artefacts from prehistoric sites (Neolithic and Iron Age), Greek colonies, sanctuaries, Roman settlements, and cemeteries. Exhibits highlights include: a) A tombstone (450-400 BC), with the deceased depicted standing with a short tunic and chlamys, bidding farewell to the world of the living ; b) a red-shaped pelike (440 BC) with representations, on one side with an Apollonian theme and on the other with a Dionysian theme ; c) a votive relief of the Thracian horseman - since 1992 the emblem of Komotini -, depicted with a spear in his right hand and on the left a tree with a coiled snake and below an altar, a wild boar and a dog, 1st century BC ; d) a sarcophagus (500 BC) with representations from Abdera ; e) an amphigraphic tombstone (500 BC) (Archaeological Museum of Athens 40 -Komotini) where the main side depicts the dead man and on the back the slave with the hunting dog. The upper part of the stele is exhibited in the National Archaeological Museum of Athens, while the one in Komotini is a replica. One of the museum's most remarkable artefacts is the golden bust of Septimius Severus (193-211 AD), brought by the imaginiferi of the Roman army.

The museum offers educational programs for elementary and middle school students, accompanied by teaching materials and specially designed brochures.