Rice and millet arrived in Western Japan from Korea around 3,000 years ago and spread eastwards across the archipelago in the next 700 years. However, the extent to which agriculture transformed traditional Jōmon hunter-gatherer-fisher communities is debated. Central Japan is a key area of study as remodelling of radiocarbon dates shows a slowdown in the dispersal rate of rice agriculture in this area. Here, we examine and compare the use of pottery by Final Jōmon and Early to Middle Yayoi communities in the Tōkai and the Central Highland regions of central Japan, using lipid residue analysis. Although the identification of specific biomarkers for rice remains elusive, an increase in the ratio of E/H C18 APAAs with the arrival of rice and millet indicates a potential change in plant processing and consumption. We were also able to identify biomarkers for broomcorn millet (miliacin) in both Final Jōmon and Yayoi pottery. However, evidence for millet consumption is sparse and in all cases was likely mixed with wild hunted and foraged foods. We conclude therefore that, despite the introduction of rice and millet agriculture in central Japan, pre-existing diets and culinary habits of Jōmon hunter-gatherers remain important.