The Developmental Origins of Health and Disease (DOHaD) framework suggests that early-life experiences affect long-term health outcomes. We tested this hypothesis by estimating the long-run effects of exposure to World War II-related food deprivation during childhood and adolescence on the risk of suffering from hypertension and type 2 diabetes at adulthood for 90,226 women from the French prospective cohort study E3N. We found that the experience of food deprivation during early-life was associated with a higher risk of developing type 2 diabetes (+0.7%, 95% CI: 0.073–1.37%) and hypertension (+2.6%, 95% CI: 0.81–4.45%). Effects were stronger for individuals exposed at younger ages. Exposed individuals also achieved lower levels of education, slept less, and were more frequently smokers than unexposed individuals. These results are compatible with both the latency and the pathway models proposed in the DOHaD framework which theorise the association between early life exposure and adult health through both a direct link and an indirect link where changes in health determinants mediate health outcomes.