: The current study aims to assess the subnational temporal trends in HIV prevalence in Malawi and Zimbabwe. Using data from three Demographic and Health Surveys (DHS) conducted in Malawi and Zimbabwe, we found that national HIV prevalence in both countries substantially declined, large declines occurred in areas where HIV prevalence was already low, and HIV prevalence in high-burden areas remained stable over time. Well designed HIV prevention programmes targeting hotspots are required for effective HIV control in countries with declining HIV prevalence.