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Here, we provide spatially continuous, high-resolution (5 m) microclimate grids covering all 923 km2 of the Bohemian Forest Ecosystem (BFE), i.e. the complete area of the Šumava (Czech Republic) and Bavarian Forest (Germany) National Parks. To derive these grids, we have established a dense network of 288 microclimatic stations that continuously measured air, near-surface, and soil temperature every 15 minutes from 12th October 2019 to 11th October 2020. We combined the measured microclimate temperature with LiDAR derived land surface topography and forest structure through boosted spatial generalized additive models (GAMs). We validated the resulting microclimatic grids with an independent network of forest weather stations and compared these microclimatic grids with the SoilTemp (soil temperature), ForestTemp (near-ground forest understorey temperature), and downscaled ERA5-Land (air temperature). The developed BFE microclimatic grids were closer to independently measured temperatures than any other alternative and captured high microclimatic variability controlled jointly by land surface topography and forest structure. Our microclimatic grids represent accurate, high-resolution spatial variation of mean annual soil temperature, mean, maximum and minimum air temperature at two heights, and growing degree days at 200 cm. The dataset contains 8 microclimatic grids (GeoTIFF format, projection EPSG 31468, resolution 5 m). Extent: 4587063, 5399139: 4646023, 5451289 The name of the file is “name.tif”, where name represents the abbreviation of the microclimatic variable (see names below). The values are in °C (°C d for GDD), the data can be readily imported into standard geographical information system software (e.g., QGIS) or accessed in a statistical software (e.g., R). The datasets do not include colour schemes. Measured variable (depth/height) - Microclimatic variable Abbreviation (Units) Soil temperature (-8 cm) - Mean temperature = mean temperature T.soil_8_cm.mean (°C) Near-ground air temperature (15 cm) - Mean temperature = mean temperature T.air_15_cm.mean (°C) - Maximum temperature = 95th percentile of daily maximum temperatures T.air_15_cm.max.95p (°C) - Minimum temperature = 5th percentile of daily minimum temperatures T.air_15_cm.min.5p (°C) Air temperature (200 cm) - Mean temperature = mean temperature T.air_200_cm.mean (°C) - Maximum temperature = 95th percentile of daily maximum temperatures T.air_200_cm.max.95p (°C) - Minimum temperature = 5th percentile of daily minimum temperatures T.air_200_cm.min.5p (°C) - Growing degree days = sum of degree days above base temperature (base 5°C) T.air_200_cm.GDD5 (°C d) Detailed description will be available in open discussion in ESSD Journal.