Despite significant research, the direct and indirect causes of a population decline in the eponymous foragers of the Late Jōmon period (c. 4500–2300 BP) in Japan remains undetermined. Here, the authors examine the impact of nutritional stress, using scurvy as a case study, on Middle and a Late/Final Jōmon populations. While an increase in the prevalence of scurvy between the time periods is apparent, no associated change in age at death was observed. The authors argue that the Late Jōmon adapted their food-sharing practices in times of ecological stress, and they highlight the need to consider morbidity and mortality together in palaeopathological assessments and the growing evidence for a non-nutritional cause in the Late Jōmon population decline.