This paper reports on diet variability in the Dogon Country (Mali) through a bio-archaeological study of pre-Dogon and early Dogon human remains (7th c. to 19th c. AD) from collective burial caves in the Bandiagara Escarpment. 220 crania from collections curated in Leiden, Paris and Bamako were studied for dental diseases. In a subset of teeth (n = 175), δ13C and δ15N were measured in bulk dentine samples. δ13C and δ15N values vary widely (-15.4 to -6.0‰ for δ13C, 6.0 to 14.8‰ for δ15N, n = 175), and indicate diets dominated by C4-based foods with a focus on plants; animal products played a minor role. There are significant differences between the δ13C values from older (pre-Dogon) and younger (Dogon) periods. Frequencies of caries, AMTL and abscesses increase significantly through time. Individuals from northern caves have more positive δ13C and δ15N values than southern ones. The temporal shifts are probably due to progressive diversification of foods, consistent with archaeological evidence showing the addition of rice and vegetables to pearl millet. The geographical disparity is explained by a combination of climatic, environmental and cultural factors. Last, inter-site differences imply that different communities (or sub-sections thereof) disposed of their dead in different caves. Based on a large sample extending over a wider area and longer time frame than previous work, our study shows that diets in the Dogon Country were neither uniform nor continuous through time, as previously proposed. Our results attest to a complex history of settlement and foodways.