The catastrophic nuclear meltdowns at Fukushima triggered a worldwide demand for renewable energy. As one of the few countries, Germany decided on an accelerated shift towards green energy, resulting in substantial conflicts with international conservation goals. Currently, large numbers of wind power facilities are erected in Germany, yet with unforeseen consequences for wildlife, particularly for endangered and protected bats. Presumably, more than 250,000 bats are killed annually due to interactions with German wind turbines, and total losses may account for more than two million killed bats over the past 10 years, if mitigation measures were not practiced. More than 70 % of killed bats are migrants, because major migratory routes cross Germany. Consequently, Germany’s environmental policy is key to the conservation of migratory bats in Europe. Prospective increases in wind power will lead to the installation of larger wind turbines with potentially devastating consequences for bats. The higher net energy production of modern wind turbines at low wind speeds may exacerbate the conflict between green energy and conservation goals since revenue losses for companies increase. We conclude that evidence-based action plans are urgently needed to mitigate the negative effects of the operation of wind energy facilities on wildlife populations in order to reconcile environmental and conservation goals.