The development of the modern industrialized food production system has resulted in a homogeneous human diet worldwide. However, it is not clear whether a developed food production system led to a homogenized human diet also in ancient societies. Due to the lack of large archaeological datasets, we know little about the chronological trends and ancient circumstances of dietary homoge-nization. Here we compiled carbon and nitrogen stable isotope ratios, indicators of palaeodiet, of adult human skeletons from premodern mainland Japan (AD 1603–1868, n = 318) to investigate chronological changes in diet. Comparison with datasets from Japan in modern, premodern (Edo), and foraging (Jomon) periods showed that the human diet was rapidly homogenized isotopically in modern times. Premodern people in Japan typically obtained dietary proteins from C3 crops and fish, and the estab-lishment of agriculture created a new isotope dietary niche compared with the foraging period. Domi-nant protein contributions from agricultural C3 crops cultivated with organic fertilizers and/or rice that are grown in paddy fields with denitrification increased premodern human nitrogen isotope ratios without increasing their carbon isotope ratios. Diet differed according to the social status of individuals or the availability of foods, and a unique diet can be seen in people in higher social classes such as the Shogun family. Meta-analysis of stable isotope ratios of archaeological human skeletons enables a comprehensive understanding of human dietary change through time and regional variations.