Land cover change is a dynamic phenomenon driven by synergetic biophysical and socioeconomic effects. It involves massive transitions from natural to less natural habitats and thereby threatens ecosystems and the services they provide. To retain intact ecosystems and reduce land cover change to a minimum of natural transition processes, a dense network of protected areas has been established across Europe. However, even protected areas and in particular the zones around protected areas have been shown to undergo land cover changes. The aim of our study was to compare land cover changes in protected areas, non-protected areas, and 1 km buffer zones around protected areas and analyse their relationship to climatic and socioeconomic factors across Europe between 2000 and 2012 based on earth observation data. We investigated land cover flows describing major change processes: urbanisation, afforestation, deforestation, intensification of agriculture, extensification of agriculture, and formation of water bodies. Based on boosted regression trees, we modelled correlations between land cover flows and climatic and socioeconomic factors. The results show that land cover changes were most frequent in 1 km buffer zones around protected areas (3.0% of all buffer areas affected). Overall, land cover changes within protected areas were less frequent than outside, although they still amounted to 18,800 km2 (1.5% of all protected areas) from 2000 to 2012. In some parts of Europe, urbanisation and intensification of agriculture still accounted for up to 25% of land cover changes within protected areas. Modelling revealed meaningful relationships between land cover changes and a combination of influencing factors. Demographic factors (accessibility to cities and population density) were most important for coarse-scale patterns of land cover changes, whereas fine-scale patterns were most related to longitude (representing the general east/west economic gradient) and latitude (representing the north/south climatic gradient).