Here we present the first high-resolution continuous palaeoecological study from Greece covering the Mesolithic–Neolithic transition at Limni Zazari, a small lake in western Macedonia. We study how interactions between vegetation and climate might have affected the introduction of agriculture to Europe ca. 8500 years ago. We found that mixed deciduous oak woodlands established around the lake once moisture availability began to increase at ~10,300 cal yr BP. Between 8600 and 8000 cal yr BP, climate change, causing drier conditions, led to the decline of the woodlands and the expansion of steppe and grassland vegetation. Concurrently, in agreement with the archaeological record, pollen indicative of arable and pastoral farming indicate the onset of Neolithic farming. After 8000 cal yr BP the forest composition changed, with a major expansion of pine forests and increases in disturbance-adapted trees like Ostrya and Fagus. This change might be linked to changes in moisture availability, but it is likely that land use also facilitated these shifts. We conclude that the introduction of Neolithic farming was advantaged by climate-induced vegetation changes. While the vegetation structure around Zazari was very sensitive to changes in moisture, early anthropogenic disturbances led to changes in the vegetation composition that are still important today.