The Kungur forest-steppe is the northernmost outpost of European forest-steppe, located in the western pre-Urals within the boreal climatic zone. The co-existence of boreal, nemoral and steppe species with relicts and endemics results in a high plant diversity, making it an important biodiversity hotspot. Under current climate change and strong agricultural impacts, the Kungur forest-steppe is rapidly degrading. In order to develop sustainable management strategies, we studied the vegetation history over the last 3500 years in the natural reserve area Spasskaya Gora. Palynological data indicate that the territory of Spasskaya Gora was largely covered by hemiboreal forests with high proportion of elm during the late Holocene. An opening of the vegetation strongly correlates with erosion, both indicating anthropogenic activities such as lumbering, agriculture, grazing and hay making. The modern Pinus and Betula dominated forests combined with large areas dominated by grasses and herbs appear in the last 300 years and caused by human activity. The data support the ‘anthropogenic’ hypothesis of the Kungur forest-steppe development, suggesting that Pleistocene steppe was replaced by hemiboreal forests during the Holocene. Steppe elements survived on exposed rocks. The recent forest-steppe landscapes dominated by pioneer birch and poplar were formed due to anthropogenic deforestation. With respect to nature conservation, our data demonstrate that prohibition of any anthropogenic activities at Spasskaya Gora will lead to loss of diversity of steppe assemblages over the mid-term. We emphasize that conservation of the high plant diversity of the Kungur forest-steppe must include disturbance factors in the form of selective lumbering, prescribed burning, moderate grazing or traditional mowing.