Ecological physiology examines how animals cope with changing environmental demands. In low-productivity desert habitats, small mammals should consume low-quality, high-fiber food as a consequence of necessity rather than by choice. Diet quality of populations can differ at both spatial and temporal scales. Nevertheless, spatial and temporal variation in the digestive system has not been extensively studied in the field. We captured individuals from 4 populations of Microcavia australis and measured their digestive morphological traits. Fieldwork was carried out in 4 localities belonging to arid and semiarid regions, in dry and wet seasons. We also estimated diet quality for each population and season. We found significant effects of sex, season, and site on the size of digestive organs. The concentration of fiber and nitrogen in the plants consumed differed between populations and varied seasonally: dietary fiber was higher in the dry season and nitrogen concentration was higher in the wet season. As predicted by theory, the cecum, the organ most closely related to cellulose fermentation, was significantly larger in animals facing the lowest quality diet. The other organs also were affected by reproductive state and water requirements. Intraspecific variation in the digestive morphology of M. australis probably helps this species cope with remarkable seasonal and geographical variability.