The Medieval Collection encompasses a diversity of artefacts, all witness to historical continuity and the broad range of cultures that shaped life on the peninsula. The collection includes Early Christian stone monuments (altar screens, sarcophagi, ciboria, ambos, mosaics, capitals), jewellery, parts of costumes, and utilitarian objects made of metal, ceramics, bone, and glass.

Early Christian and early medieval churches in Pula (St John at the Nymphaeum, St Felicitas, St Catherine), Nesactium, and near Galižana (St Peregrinus, St Zeno, St Lucy) saw archaeological investigation during the Austro-Hungarian administration. Exceptionally valuable Early Christian reliquaries were found in the churches of St Thomas and St Hermagoras (now kept in Vienna and Venice). Mosaics pavements and Early Christian and Medieval sacral inventory from across the early Pula diocese were displayed as part of the museum's collection of stone sculpture in the period between the two World Wars.

A medieval department was created in the frame of AMI in the period following the Second World War. A collection of stone sculpture was established at Pula's St Francis monastery building featuring Pre-Romanesque and Romanesque sculpture drawn from the Vodnjan collection of stone sculpture and from other churches in the south of Istria. There was a particular effort to archaeologically investigate church buildings, including St Sophia's in Dvigrad, The Assumption of Mary's near Bale, St Michael's near Vodnjan, and St Andrew's near Betiga. Artefacts recovered during excavations of late antiquity period graves (Škicini, Betegenica, Frančini) and churches (St. Elisha's, St Nicholas'), castles (Gočan, Kočur, Sipar), and early Slavic and early Croatian cemeteries (near Novigrad, Motovun, Ferenci, Buzet, Žminj, Buje) provided new insights into the period of Early Byzantine and Frankish rule in Istria. This set the stage for the systematic presentation of the Early Medieval period in the AMI permanent exhibition as of 1973. Field investigations and conservation interventions were carried out for the presentation of the remains of churches at the Nesactium site, in Betiga, Valbandon, Ližnjan, and at the St Mary Formosa basilica site.