The commonly held belief that the emergence and establishment of farming communities in the Levant was a smooth socio-economic continuum during the Pre-Pottery Neolithic (ca. 12,000-9,000 cal BP) with only rare minor disruptions is challenged by recently obtained evidence from this region. Using a database of archaeological radiocarbon dates and diagnostic material culture records from a series of key sites in the northern Levant we show that the hitherto apparent long-term continuity interpreted as the origins and consolidation of agricultural systems was not linear and uninterrupted. A major cultural discontinuity is observed in the archaeological record around 10,000 cal BP in synchrony with a Holocene Rapid Climate Change (RCC), a short period of climatic instability recorded in the Northern Hemisphere. This study demonstrates the interconnectedness of the first agricultural economies and the ecosystems they inhabited, and emphasizes the complex nature of human responses to environmental change during the Neolithic period in the Levant. Moreover, it provides a new environmental-cultural scenario that needs to be incorporated in the models reconstructing both the establishment of agricultural economy in southwestern Asia and the impact of environmental changes on human populations.