The Mesolithic to Neolithic transition in Europe marked the transition of humans from hunter-gathers to agriculturalists. This event coincided with rising sea levels in the area and submergence of numerous paleosols, obscuring the earliest evidence of the transition from the archaeological record. A combination of archaeological and molecular approaches of sediment cores dating from 8030-7980 cal BP show the presence of domesticated plant species, suggesting neolithicisation of the area 2,000 years earlier than expected. The submitted raw sequence data here correspond to four strata of a core sample within this time range. Using a shotgun metagenomic approach we identified sequences of domesticated plant species amongst background ecology of the early Neolithic, around 8,000 cal BP.