The coronavirus disease 2019 (COVID-19)-related excess mortality in Switzerland is well documented, but no study examined mortality at the small-area level. We analysed excess mortality in 2020 for 2141 Swiss municipalities using a Bayesian spatiotemporal model fitted to 2011-19 data. Areas most affected included the Ticino, the Romandie and the Northeast. Rural areas, municipalities within cross-border labour markets, of lower socioeconomic position and with less support for control measures in the popular vote on the COVID-19 Act had greater excess mortality. Particularly vulnerable municipalities require special efforts to mitigate the impact of pandemics.