From northern China, millet agriculture spread to Korea and the Maritime Russian Far East by 3500–2700 BC. While the expansion of agricultural societies across the Sea of Japan did not occur until around 900 BC, the intervening period saw major transformations in the Japanese archipelago. The cultural florescence of Middle Jōmon central Honshu underwent a collapse and reorganisation into more decentralised settlements. Mobility increased as Late Jōmon influences spread from eastern into western Japan, and populations expanded to offshore islands such as Okinawa and the Kurils. In Kyushu and other parts of western Japan, the eastern Jōmon expansion was associated with the cultivation of adzuki and soybeans but, contrary to earlier assessments, there is no evidence for the introduction of cereal crops at this time. Here, we analyse archaeological and historical linguistic evidence of connections between the Eurasian mainland and the Japanese Islands c. 3500 to 900 BC. A re-evaluation of archaeological material discussed since the 1920s concludes that the transformations in Jōmon society during this period were at least in part a response to contacts with Eurasian Bronze Age cultures. Evidence for linguistic contact between Koreanic and the Ainuic languages which are presumed to have been spoken by Jōmon populations is also consistent with new Bronze Age mobilities. Although prehistoric Japan was one of the most isolated regions of Eurasia, we conclude that the historical evolution of societies in the Japanese archipelago after the third millennium BC was linked with processes of Bronze Age globalisation.