Climate data matching the scales at which organisms experience climatic conditions are often missing. Yet, such data on microclimatic conditions are required to better understand climate change impacts on biodiversity and ecosystem functioning. Here we combine a network of microclimate temperature measurements across different habitats and vertical heights with a novel radiative transfer model to map daily temperatures during the vegetation period at 10 m spatial resolution across Switzerland. Our results reveal strong horizontal and vertical variability in microclimate temperature, particularly for maximum temperatures at 5 cm above the ground and within the topsoil. Compared to macroclimate conditions as measured by weather stations outside forests, diurnal air and topsoil temperature ranges inside forests were reduced by up to 3.0 and 7.8 ^∘C, respectively, while below trees outside forests, e.g. in hedges and below solitary trees, this buffering effect was 1.8 and 7.2 ^∘C, respectively. We also found that, in open grasslands, maximum temperatures at 5 cm above ground are, on average, 3.4 ^∘C warmer than those of the macroclimate, suggesting that, in such habitats, heat exposure close to the ground is often underestimated when using macroclimatic data. Spatial interpolation was achieved by using a hybrid approach based on linear mixed-effect models with input from detailed radiation estimates from radiative transfer models that account for topographic and vegetation shading, as well as other predictor variables related to the macroclimate, topography, and vegetation height. After accounting for macroclimate effects, microclimate patterns were primarily driven by radiation, with particularly strong effects on maximum temperatures. Results from spatial block cross-validation revealed predictive accuracies as measured by root mean squared errors ranging from 1.18 to 3.43 ^∘C, with minimum temperatures being predicted more accurately overall than maximum temperatures. The microclimate-mapping methodology presented here enables a biologically relevant perspective when analysing climate–species interactions, which is expected to lead to a better understanding of biotic and ecosystem responses to climate and land use change.