The Middle Stone Age (MSA) of eastern Africa has a long history of research and is accompanied by a rich fossil record, which, combined with its geographic location, have led it to play an important role in investigating the origins and expansions of Homo sapiens. Recent evidence has suggested an earlier appearance of our species, indicating a more mosaic origin of modern humans, highlighting the importance of regional and inter-regional patterning and bringing into question the role that eastern Africa has played. Previous evaluations of the eastern African MSA have identified substantial variability, only a small proportion of which is explained by chronology and geography. Here, we examine the structure of behavioural, temporal, geographic and environmental variability within and between sites across eastern Africa using a quantitative approach. The application of hierarchical clustering identifies enduring patterns of tool use and site location through the MSA as well as phases of significant behavioural diversification and colonisation of new landscapes, particularly notable during Marine Isotope Stage 5. As the quantity and detail of technological studies from individual sites in eastern Africa gathers pace, the structure of the MSA record highlighted here offers a roadmap for comparative studies.