Research on the combined effects of climate change and nitrogen deposition on reproductive traits, and especially on the production of viable seeds, is still scarce despite their importance for population persistence and expansion. Hence, in this study we set out to investigate the direct and indirect effects of the above-mentioned global change drivers on seed viability in the coniferous shrub Juniperus communis L. In many parts of its European range, juniper is increasingly threatened, partly because of a lack of sexual reproduction. We hypothesised that this regeneration failure is partly due to poor seed viability. Using data from 39 populations throughout Europe, we were able to demonstrate that a strong, triangular-shaped relationship exists between the percentage of viable seeds produced and the percentage of juniper seedlings occurring in a population, which indicates that the species is indeed partly seed limited. Furthermore, based on an extended dataset of 42 populations, we found that seed viability was negatively affected by temperature, measured as mean annual growing degree-days, and nitrogen deposition (but not by drought). Suggestions are made about the processes behind the observed patterns, but more research is required. Nevertheless, our results do raise serious concerns for the conservation of juniper in light of the predicted rise in temperature and global nitrogen emissions. Furthermore, it is likely that similar patterns can also be observed for other species.