Archaeological evidence from dry cave deposits in the northern Chihuahuan Desert reveal intensive utilisation of desert plants that store prebiotic inulin-type fructans as the primary carbohydrate. In this semi-arid region limited rainfall and poor soil conditions prevented the adoption of agriculture and thus provides a unique glimpse into a pure hunter-forager economy spanning over 10 000 years. Ancient cooking features, stable carbon isotope analysis of human skeletons, and well-preserved coprolites and macrobotanical remains reveal a plant-based diet that included a dietary intake of about 135 g prebiotic inulin-type fructans per d by the average adult male hunter-forager. These data reveal that man is well adapted to daily intakes of prebiotics well above those currently consumed in the modern diet.