Knowledge of historic changes in vegetation, relief, and soil is key in understanding how the uplands in central Europe have changed during the last millennium, being an essential requirement for measures on forest conversion and nature conservation in that area. Evidence of forest‐clearing horizons from the medieval period could be systematically documented at four low‐ to mid‐altitudinal sites (360–640 meters above mean sea level) in the Harz (Harz Mountains), Erzgebirge (Ore Mountains), and Českomoravská vrchovina (Bohemian‐Moravian Highlands). Subfossil trees with traces of human cutmarks and burning were recovered from buried wet‐organic soils (paleosols) within a context of mining and settlement archaeology, applying a multiproxy‐approach by using data from archaeology, paleobotany, geochronology, dendrochronology, and pedology. Tree stumps and trunks, as well as small‐scale wood remains represent an in situ record of local conifer stands (spruce, fir, and pine). Some deciduous tree taxa also occur. Dating of the tree remains yielded ages from the 10th/11th to the 13th/14th centuries A.D. After deforestation, the tree remains were buried by technogenic and alluvial–colluvial deposits. The reconstructed conifer‐dominated woodlands on wet soils mirror the local vegetation structure immediately before the medieval deforestation. As such wet sites are common in the uplands, conifers were significantly present in the natural vegetation even at mid and lower altitudes.