Temperatures in high-mountain areas have increased rapidly during recent decades. However, how this overall warming trend has translated into microclimatic conditions that the specialised alpine organisms experience remains largely unknown due to the lack of microclimatic data across large spatial and temporal scales. Here, we present a reconstruction of local-scale topsoil temperatures for the alpine zone of the European Alps. We employ a mechanistic microclimate model to calculate hourly topsoil temperatures across four decades, based on extensive macroclimate reanalysis, edaphic, topographic, and vegetation data. These microclimatic data will allow us to identify microhabitats thermally distinct from the surrounding landscapes, as well as their specific temperature trends, and to assess the existence of potential microrefugia that might safeguard cold-adapted alpine biodiversity in the course of ongoing climate change.