Being overweight and obesity are emerging public health issues in sub-Saharan Africa. Currently, there is limited knowledge on the temporal trend of the effect of socioeconomic factors and air quality on being overweight or obesity. Using data from the Ugandan Demographic and Health Survey and NASA’s Socioeconomic Data and Applications Center (SEDAC), we examined the spatio-temporal effect of individual and contextual factors on overweight and obesity among women in Uganda using cross-sectional data on 15,655 women in Uganda. We employed multilevel mixed-effect analysis and Bayesian hierarchical spatial models to examine the effect of individual socioeconomic status, contextual socioeconomic factors and air quality on women’s risk of being overweight or obese as well as investigate spatial heterogeneity in the association. The prevalence of overweight/obesity for the study periods were 17.23% (2000/2001), 15.36% (2006), 19.36% (2011) and 21.93% (2016). The result from the multilevel analysis shows change in the directions of the association between individual factors (educational status and household wealth) and overweight or obese over the years. Women with secondary education were 1.514 times (p = 0.002) more likely to be overweight or obese in the 2000/2001 group but 0.655 times (p = 0.007) less likely to be overweight or obese in the 2016 group. It also reveals temporal consistency in the effect of the air pollutant PM2.5 on overweight or obese. The spatial models reveal spatial heterogeneity in the association between district-level factors and the proportion of overweight or obese women. The findings suggest improving women’s socioeconomic status and air quality could reduce the rising obesity epidemic in Ugandan women.