The effect of dietary fibre and starch content on digestibility, microfaunal population and caecal function was investigated in a subterranean mole-rat, Heterocephalus glaber (Rodentia). Mole-rats were fed on a diet of either sweet potato (neutral-detergent fibre (NDF) 65 g/kg dry matter (DM), starch 638 g/kg DM) or carrot (NDF 157 g/kg DM, starch 258.7 g/kg DM) for 4 weeks. Daily intake and faecal output were monitored. Thereafter caecal microfaunal population, density and function were assessed using light and scanning electron microscopy and by measuring both gas and short chain fatty acid (SCFA) production. A 2.4-fold increase in fibre and 2.5-fold decrease in starch content resulted in a decrease in caecal DM content (390 g/kg). A concomitant dramatic decline (by 93%) in ciliate protozoa with a corresponding 2-fold increase in bacteria also accompanied this change in diet. Fermentative efficiency as indicated by gas production was 2.6 times greater on a carrot diet than on sweet potato. Microbial fermentation resulted in higher SCFA concentrations on the carrot diet, with a 42% reduction in SCFA concentration on the sweet potato diet. Here, SCFA contributed 5.1% of daily energy expenditure and this increased 5.0-fold on the carrot diet. Caecal micro-organism function, therefore, played an important role in the nutritional physiology of these naked mole-rats, and enabled maximum utilization of the food substrate.