Wind farms and their associated transmission infrastructure can have negative impact on biodiversity. Offshore wind farms, for example, can pose threats to animals like harbour porpoises and migrating birds and onshore wind farms and transmission grids may harm birds and bats. In this article we analyse how European Union species protection law is transposed and applied to decision-making on wind energy projects in five member states, namely Denmark, Germany, the Netherlands, Belgium and the United Kingdom. The analysis aims to understand the differences in the interpretation and application of national species protection law, point out deficiencies, and make recommendations, partly based on learning from best practices. Though transposition in national law is almost identical, implementation practice in these states varies substantially. The question is raised whether the legal regime, as currently applied, can be improved to serve the aims of a considerable increase of renewable energy sources whilst simultaneously protecting biodiversity.