In natural corundum, a strong geochemical correlation is sometimes observed between Be and heavy high field strength elements (HHFSEs) such as Nb, Ta and W, and it has been hypothesized that trace elements are hosted in primary inclusions. However, no known mineral enriched in both Be and HHFSEs stable at these geological conditions can explain this correlation. To understand how Be and HHFSEs are distributed in natural corundum down to the atomic scale, two natural Be-bearing sapphire crystals from Afghanistan and Nigeria are studied using laser ablation inductively coupled plasma and time-of-flights secondary ion mass spectrometry, atom probe tomography and transmission electron microscopy. In addition to common trace elements such as Mg, Ti, and Fe, Be and W are detected in the metamorphic sapphire from Afghanistan, whereas Be, Nb and Ta are detected in the magmatic sapphire from Nigeria. Nanoclustering in both samples shows fractionation of Be and high field strength elements (including Ti) by atomic mass, suggesting a secondary process controlled by solid-state diffusion. The homogeneously distributed W and the secondary nano-precipitates bearing Nb and Ta indicates that HHFSEs can be incorporated into the corundum structure during crystallization, most likely through preferred adsorption on the growth surface. The strong correlation between Be and HHFSEs across the growth zones is probably due to Be being attracted by HHFSEs to partially balance the charge when incorporated into the corundum structure. The enrichment of high field strength elements by growth kinetics may result in supersaturated concentrations during crystallization, allowing them to precipitate out when the host corundum is heated above its formation temperature by basaltic magma. Comparison with previous transmission electron microscope studies suggests the same process for incorporating Be and HHFSEs also applies to other natural corundums from different localities.