Drought affects more people than any other natural disaster but there is little understanding of how ecosystems react to droughts. This study jointly analyzed spatio-temporal changes of drought patterns with vegetation phenology and productivity changes between 1999 and 2010 in major European bioclimatic zones. The Standardized Precipitation and Evapotranspiration Index (SPEI) was used as drought indicator whereas changes in growing season length and vegetation productivity were assessed using remote sensing time-series of Normalized Difference Vegetation Index (NDVI). Drought spatio-temporal variability was analyzed using a Principal Component Analysis, leading to the identification of four major drought events between 1999 and 2010 in Europe. Correspondence Analysis showed that at the continental scale the productivity and phenology reacted differently to the identified drought events depending on ecosystem and land cover. Northern and Mediterranean ecosystems proved to be more resilient to droughts in terms of vegetation phenology and productivity developments. Western Atlantic regions and Eastern Europe showed strong agglomerations of decreased productivity and shorter vegetation growing season length, indicating that these ecosystems did not buffer the effects of drought well. In a climate change perspective, increase in drought frequency or intensity may result in larger impacts over these ecosystems, thus management and adaptation strategies should be strengthened in these areas of concerns.