[1][2] In 1925, a museum depot was formed in two rooms of the madrasa within the Sultan Bayezid II Complex when a few archaeological artifacts and some Islamic era mummies were stored up together.

As more space became needed due to the increased number of items for exhibition, the inventory was transferred in 1962 to the 13th-century monumental Seljuk era-building at Gökmedrese Mosque.

[2] The archaeological section in the upper floor contains artifacts unearthed inat local archaeological excavations, including earthenware, bronze daggers and axes, needles, loom weights and seals of the Early Bronze Age (3500–2100 BC) and Hittites (1400–1200 BC), figurine of Hittite storm deity Teshub, best known as the Amasya figurine, acquired bronze bracelets and pots of Kingdom of Urartu (900–600 BC), libation bowls of Phrygians (850–600 BC), iron sword and diverse metallic fighting tools of a Scythian cavalry (6th century BC), dishes and kantharos from the Hellenistic period, tear catchers, glass perfume cups, bowls, terracotta kantharos, theatrical masks, bronze containers, various golden, silver and glass women's jewellery of the Roman era, Hellenistic and Roman oil lamps and bronze coins, copper coins of Byzantine, silver coins of Seljuk and golden coins of Ottoman period, and finally diverse Byzantine period (476-1453 AD) items.

[2] In the garden to the west of the museum, large-sized stone artifacts are on display from the periods of Hittites, Hellenistic, Byzantine, Ilkhanate, Seljuk and Ottoman.

These are Hittite gate lion statues, Hellenistic and Roman epigraphies, Ionic order and Corinthian order capitals, Roman sarcophagi made of marble and limestone, inscriptions and milestones, Byzantine steles and architectural elements as well as inscriptions of buildings, headstones, terracotta jars and mosque column capitals from the Ilkhanate, Seljuk and Ottoman periods.