BackgroundCOVID-19 vaccination efforts are lagging in Sub-Saharan Africa, as just over 20 percent of the population has been fully vaccinated. COVID-19 vaccine hesitancy is considered important as a prerequisite for widespread vaccine take-up. Here, we study the dynamics of vaccine acceptance, its correlates, and reasons for hesitancy over time, drawing on two years of panel survey data.MethodsIn this observational study, we use multiple rounds of data from national High Frequency Phone Surveys (HFPS) in five countries in East and West Africa (Burkina Faso, Ethiopia, Malawi, Nigeria, and Uganda), covering a period between 2020 and 2022. The surveys are cross-country comparable and draw their samples from nationally representative sampling frames. Based on this data source, the study presents population-weighted means and performs multivariate regression analysis.ResultsCOVID-19 vaccine acceptance was high throughout the study period (68% to 98%). However, acceptance levels were lower in 2022 than in 2020 in three countries (Burkina Faso, Malawi, Nigeria), and higher in one country (Uganda). Moreover, individuals are observed to change their stated vaccine attitudes between survey rounds, to a limited extent in some countries (Ethiopia) and more frequently in others (Burkina Faso, Malawi, Nigeria, Uganda). Vaccine hesitancy is higher in richer households, and those residing in urban areas; among women and those better educated. Hesitancy is lower in larger households and among heads of the household. The main reasons for hesitancy are concerns about side effects of the vaccine, its safety and efficacy, as well as assessments of COVID-19 risk, though these reasons fluctuate over time.ConclusionsReported COVID-19 vaccine acceptance levels remain far above vaccination rates in the study countries, suggesting that vaccine hesitancy is not the primary obstacle to reaching greater vaccine coverage, which may instead be related to access and delivery barriers as well as supply shortages. Nevertheless, vaccine attitudes appear malleable so that continued efforts are needed to retain high levels of vaccine acceptance.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12919-023-00266-x.