Climate change resulting from the enhanced greenhouse effect together with the direct effect of increased atmospheric CO2 concentrations on vegetation growth are expected to produce changes in the cycling of carbon in terrestrial ecosystems. Impacts will vary across Europe, and regional-scale studies are needed to resolve this variability. In this study, we used the LPJ-GUESS ecosystem model driven by a suite of regional climate model (RCM) scenarios from the European Union (EU) project PRUDENCE to estimate climate impacts on carbon cycling across Europe. We identified similarities and discrepancies in simulated climate impacts across scenarios, particularly analyzing the uncertainties arising from the range of climate models and emissions scenarios considered. Our results suggest that net primary production (NPP) and heterotrophic respiration (Rh) will generally increase throughout Europe, but with considerable variation between European subregions. The smallest NPP increases, and in some cases decreases, occurred in the Mediterranean, where many ecosystems switched from sinks to sources of carbon by 2100, mainly as a result of deteriorating water balance. Over the period 1991–2100, modeled climate change impacts on the European carbon balance ranged from a sink of 11.6 Gt C to a source of 3.3 Gt C, the average annual sink corresponding with 1.85% of the current EU anthropogenic emissions. Projected changes in carbon balance were more dependent on the choice of the general circulation model (GCM) providing boundary conditions to the RCM than the choice of RCM or the level of anthropogenic greenhouse gases emissions.