The importance of understanding the long-lasting legacy of past land use on modern ecosystems has long been acknowledged. However, the magnitude and persistence of such legacies have been assessed only occasionally. Northern Greece has been a gateway of farming into mainland Europe during the Neolithic, thus providing a perfect setting to assess the potential impact of land-use history on present-day ecosystems. Additionally, the marked Holocene climatic variability of the southern Balkans makes it possible to investigate climate-vegetation-land use interactions over long timescales. Here, we have studied a sediment record from Limni Vegoritis (Northern Greece) spanning the past ∼9000 years using palaeoecological proxies (pollen, spores, stomata, microscopic charcoal). We aimed to reconstruct long-term vegetation dynamics in submediterranean Greece, to assess the environmental factors controlling them and to establish the legacies of the long history of land use in the modern landscape. We found that the Early Holocene afforestation, mainly oak woodlands, was delayed because of suboptimal moisture conditions. Later, colder and drier conditions during the rapid climate change centred around the ‘8.2 ka event’ triggered woodland opening and the spread of wooded (Juniperus) steppe vegetation. First indicators of farming activities are recorded during this period, but their abundances are too low to explain the concurrent large deforestation episode. Later, pinewoods (probably dominated by Pinus nigra) with deciduous Quercus spread and dominated the landscape for several millennia. These forests experienced repeated multi-centennial setback-recovery episodes associated with land-use intensification, but pines eventually declined ∼2500–2000 years ago during Classical times under heavy land use comprising intense pastoralism. This was the starting point for the present-day landscape, where the main ‘foundation’ taxon of the ancient forests (Pinus cf. nigra) is missing, therefore attesting to the strong imprint that historical land use has left on the modern landscape.