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Abstract Background Cardiovascular disease (CVD) is increasing in Sub-Saharan Africa (SSA). Overweight/obesity and tobacco use are modifiable CVD risk factors, however literature about the spatiotemporal dynamics of these risk factors in the region at subnational or local scales is lacking. We describe the spatiotemporal trends of overweight/obesity and tobacco use at subnational levels over a 13-year period (2003 to 2016) in five East African nations. Methods Cross-sectional, nationally representative Demographic and Health Surveys (DHS) were used to explore the subnational spatiotemporal patterns of overweight/obesity and tobacco use in Burundi, Kenya, Rwanda, Tanzania, and Uganda, five East African Community (EAC) nations with unique cultural landscapes influencing CVD risk factors. Adaptive kernel density estimation and logistic regression were used to determine the spatial distribution and change over time of CVD risk factors on a subnational and subpopulation (rural/urban) scale. Results Subnational analysis shows that regional and national level analysis masks important trends in CVD risk factor prevalence. Overweight/obesity and tobacco use trends were not similar: overweight/obesity prevalence increased across most nations included in the study and the inverse was true for tobacco use prevalence. Urban populations in each nation were more likely to be overweight/obese than rural populations, but the magnitude of difference varied widely between nations. Spatial analysis revealed that although the prevalence of overweight/obesity increased over time in both urban and rural populations, the rate of change differed between urban and rural areas. Rural populations were more likely to use tobacco than urban populations, though the likelihood of use varied substantially between nations. Additionally, spatial analysis showed that tobacco use was not evenly distributed across the landscape: tobacco use increased in and around major cities and urban centers but declined in rural areas. Conclusions We highlight the importance of de-homogenizing CVD risk factor research in SSA. Studies of national or regional prevalence trends mask important information about subpopulation and place-specific behavior and drivers of risk factor prevalence. Spatially explicit studies should be considered as a vital tool to understand local drivers of health, disease, and associated risk factor trends, especially in highly diverse yet low-resourced, marginalized, and often homogenized regions.