Caves may have been built initially in the soft volcanic rock of the Cappadocia region by the Phrygians, an Indo-European people, in the 8th–7th centuries BCE, according to the Turkish Department of Culture. When the Phrygian language died out in Roman times, replaced with its close relative, the Greek language, the inhabitants, now Christian, expanded their underground caverns adding the chapels and Greek inscriptions.
The city at Derinkuyu was fully formed in the Byzantine era, when it was heavily used as protection from Muslim Arabs during the Arab–Byzantine wars (780-1180). It was at this time that most of the chapels and Greek inscriptions were added. The city was connected with other underground cities through miles of tunnels. Some artifacts discovered in these underground settlements belong to the Middle Byzantine Period, between the 5th and the 10th centuries AD.
These cities continued to be used by the Christian natives as protection from the Mongolian incursions of Timur in the 14th century.