In order to investigate dietary changes during the Middle Ages, carbon and nitrogen isotopes were measured in 97 humans and 14 animals from the medieval centre of Stara ´ Boleslav, together with a comparative dataset of 28 humans from Prague – Loret´ansk´e Square. The Star´a Boleslav dataset was divided into three contexts based on grave location (abandoned unknown Early Medieval church, and collegiate chapter basilica) and chronology (pre- and post-1150 CE phases of the basilica burial ground).The average human ẟ13C value was − 19.2 ± 0.4 ‰ and the average ẟ15N value was 10.3 ± 1.2 ‰. There were statistically significant differences in ẟ15N values between all contexts with the exception of the abandoned church and the Prague – Loret´ansk´e Square cemeteries, which showed similarly low ẟ15N values. The post-1150 CE phase of the basilica burial ground showed the highest ẟ15N values, while the pre-1150 phase of the basilica burial ground occupied the intermediate position.The results show the almost complete absence of millet in the diet of the studied dataset, suggesting that a dietary dichotomy in millet consumption was present in the 11th century population, with the inhabitants of the centres consuming less millet than observed in previously published rural datasets.The increase in the consumption of animal products and/or fish was pronounced in the most recent phase of the dataset, after 1150 CE. Some evidence of this pattern was present even earlier, but only in the environment closely linked to the ecclesiastical centre, i.e. the basilica.