Dietary behavior in the context of the formation of state structure, Christianization, and significant urbanization was studied, using the Great Moravian Empire (9th–10th century AD, Czech Republic) as a representative example. We also analyzed the impact of the disruption of social structure at the beginning of the 10th century and subsequent recovery of society during the 11th century. Carbon and nitrogen isotopic values were measured in 189 adults (both sexes) and 74 animals representing different socio-economic contexts (power centers/hinterlands) and chronology (Great Moravian/Late Hillfort period). Statistically significant differences in animal protein consumption were observed between centers and hinterlands. For centers, significant relationship was found between nitrogen isotopic values and socio-economic status in males, but not for females. Diachronic diet changes were observed, with the 11th century diet characterized by higher millet consumption in both sexes and lower consumption of animal protein in males. These results confirm that Great Moravia represented a highly stratified society socio-economically. Social status appears to determine the consumption of animal protein much more in males than in females. The diet of females also proved to be more uniform in the diachronic frame. The diachronic change in dietary behavior suggests that through the apparent recovery in the 11th century, Moravian society did not reach its original level of welfare at least in terms of the quality of diet.