Traditionally, the classification of bees has been conducted with the aid of dissecting (light) microscopy. In more recent times, detailed information on external and internal morphology for bee classification has been obtained using scanning and transmission electron microscopy. MicroCT is emerging as a new method for non-invasive 3D computerised X-ray tomographic imaging of insects at the microscopic level and, in this study, has been evaluated for its use in morphological studies of bees. A Skyscan 1172 MicroCT system was used to assess the internal and external morphology of the Australian stingless bee Trigona carbonaria with particular focus on the proventricular plates. MicroCT was useful in non-invasively visualising gross external morphological features such as the articulations of the coxae, trochanters, tibiae and tarsi of each leg including broadened hind basitarsi. Image magnification revealed further detail such as antennal scapes and the various parts of the tongue including the proboscis and labium. However, the individual facets of the eye were barely discernable and MicroCT did not reveal fine details of hairs on the body or legs. Internal morphology was clearly visualised, including the tracheal system and details of the proventriculus and proventricular basal plates which form the leaflets of the proventricular valve. Thus, the characteristic features of the proventricular basal plates of Meliponini could be quickly and easily identified non-invasively. Therefore, MicroCT, as one of the emerging techniques of diagnostic radioentomology, has particular advantages for non-invasively and non-destructively imaging bees and, particularly, rare or more scientifically valued insects such as museum specimens and those trapped in amber.