Eastern Africa has played a prominent role in debates about human evolution and dispersal due to the presence of rich archaeological, palaeoanthropological and palaeoenvironmental records. However, substantial disconnects occur between the spatial and temporal resolutions of these data that complicate their integration. Here, we apply high resolution climatic simulations of two key parameters, mean annual temperature and precipitation, and a biome model, to produce a highly refined characterisation of the environments inhabited during the eastern African Middle Stone Age. Occupations are typically found in sub humid climates and landscapes dominated by or including tropical xerophytic shrubland. Marked expansions from these core landscapes include movement into hotter, low altitude landscapes in Marine Isotope Stage 5 and cooler, high altitude landscapes in Marine Isotope Stage 3, with the recurrent inhabitation of ecotones between open and forested habitats. Through our use of high resolution climate models, we demonstrate a significant independent relationship between past precipitation and patterns of Middle Stone Age stone tool use overlooked by previous studies. Engagement with these models not only enables spatiotemporally explicit examination of climatic variability across Middle Stone Age assemblages in eastern Africa but enables clearer characterisation of the habitats early human populations were adapted to, and how they changed through time.