This article highlights certain challenges as regards the reconciliation between concerns of climate change, energy security and biodiversity protection, drawing on case law of the Court of Justice of the European Union (CJEU) and the Danish experiences regarding onshore wind energy installations. The EU species protection rules are by many perceived as an obstacle to wind energy development as also reflected in the 2022 Commission proposal to amend the Renewable Energy Directive. However, it is not evident that the proposal will solve the challenges of accommodating the strict direct species protection of, in particular, Annex IV species and birds against deliberate killing or disturbance as determined by the CJEU. The article suggests that rather than setting aside the general environmental impact assessment (EIA) and appropriate assessment requirements for Natura 2000 sites, there is a need to revisit the Birds and Habitats Directives, in particular as regards ‘deliberate killing or disturbance’ caused by non-intentional activities with a view to the population level as opposed to the individual specimen level.