The Medieval Collection encompasses diverse archaeological finds as witnesses to historical continuity and varied cultural influences on the peninsula. The collection includes Early Christian stone monuments (altar screens, sarcophagi, ciboria, ambos, mosaics, capitals), jewelry, parts of costumes, and utilitarian objects made of metal, ceramic, bone, and glass. 

During the Austro-Hungarian period, Early Christian and Early Medieval churches in Pula (St. John of the Nymphaeum, St. Felicita, St. Catherine), in Nesactium, and near Galižana (St. Peregrine, St. Zeno, St. Lucy) were explored. Exceptionally valuable Early Christian reliquaries were found in the churches of St. Thomas and St. Hermagoras (today in Vienna and Venice). Between the two World Wars, floor mosaics and monuments of Early Christian and Medieval sacral inventory from the territory of the early Pula diocese were displayed in the museum's lapidarium at the time. 

After the Second World War, the Medieval Department of the AMI was established. In the monastery of St. Francis in Pula, a lapidarium was set up with Pre-Romanesque and Romanesque monuments from the so-called Vodnjan lapidarium and other churches in southern Istria. Special attention was paid to the research of churches, such as the church of St. Sophia in Dvigrad, Vele Gospa near Bale, the church of St. Michael near Vodnjan, and the church of St. Andrew near Betiga. Finds from new field excavations of Late Antique graves (Škicini, Betegenica, Frančini) and churches (St. Elizej, St. Nicholas), castles (Gočan, Kočur, Sipar), and Old Slavic and Old Croatian cemeteries (near Novigrad, Motovun, Ferenci, Buzet, Žminj, Buje) provided additional insights into the period of Early Byzantine and Frankish rule in Istria. This enabled a systematic presentation of the Early Medieval period in the museum's permanent exhibition from 1973. Field research and conservation interventions were carried out for the presentation of the remains of churches in Nesactium, Betiga, Valbandon, Ližnjan, and the basilica of St. Mary Formosa.