Agios Nikolaos was settled in the late Bronze Age by Dorian occupants of Lato under the name Lato pros Kamara, often simply Kamara. It was the port of Lato for a long time. In the 2nd century BC, Lato was abandoned, and many citizens settled in Kamara. The name of the present-day town comes from the church of Agios Nikolaos, which dates back to the 9th or 10th century and is one of the oldest intact churches in Crete.

In 1970, the Archaeological Museum was opened to house finds from Eastern Crete that had previously been housed in Heraklion

Clay figurines from Minoan peak sanctuaries. Protopalatial period (2000 - 1700 BC)