The development of farming was a catalyst for the evolution of the human diet from the varied subsistence practices of hunter-gatherers to the more globalised food economy we depend upon today. Although there has been considerable research into the dietary changes associated with the initial spread of farming, less attention has been given to how dietary choices continued to develop during subsequent millennia. A paleogenomic time transect for 5 millennia of human occupation in the Great Hungarian Plain spanning from the advent of the Neolithic to the Iron Age, showed major genomic turnovers. Here we assess where these genetic turnovers are associated with corresponding dietary shifts, by examining the carbon and nitrogen stable isotope ratios of 52 individuals. Results provide evidence that early Neolithic individuals, which were genetically characterised as Mesolithic hunter-gatherers, relied on wild resources to a greater extent than those whose genomic attributes were of typical Neolithic European farmers. Other Neolithic individuals and those from the Copper Age to Bronze Age periods relied mostly on terrestrial C3 plant resources. We also report a carbon isotopic ratio typical of C4 plants, which may indicate millet consumption in the Late Bronze Age, despite suggestions of the crop's earlier arrival in Europe during the Neolithic.