Nest structures of the Australian blue-banded bee, Amegilla holmesi Rayment (Hymenoptera: Apidae), are difficult to monitor non-invasively, because the bee is a fossorial species that constructs tunnels and natal cells within the soil. Visualization of nest structures requires physical separation of the structures from the soil substrate, which destroys the nest. Using helical, two-dimensional (2D) X-ray computerized tomography (CT), and three–dimensional (3D) volume rendering software on 13 artificial mud-brick nests, we were able to view all previously reported nest structures and cell contents without damaging the nests. We used three volume rendering algorithms (sum along ray, scatter HQ, and false colour), two of which (scatter HQ and false colour) have not previously been used to visualize nest architecture. Each algorithm has a particular advantage for visualizing specific nest structures. The 2D CT images provided the greatest spatial resolution within and between nest structures (capture pixel matrix size 512 × 512; voxel size 0.449 mm3), and for the first time we were able to visualize a meniscus within natal cells that contained liquid provisions, which is a valuable characteristic in detecting the earliest stage of juvenile development once a natal cell is sealed. We also recorded and attributed Hounsfield units to nest structures and their contents that can be utilized in future studies. This new method also enabled us to count and measure natal cells using on-screen linear callipers, visually observe and record stages of larval and pupal development, and visually gauge the incidence of cell parasitism without damaging the nest. Artificial nests can be transported easily to research facilities that have CT scanners; each scan including image processing takes less than 30 min per nest and currently costs less than AUD 20.00, which is within the reach of apiculturists. X-ray CT could be used to follow the life cycle of blue-banded bees and other cryptic species and also to monitor their health.