Wind energy is the leading renewable technology towards achieving climate goals, yet biodiversity trade-offs via land take are emerging. Thus, we are facing the paradox of impacting on biodiversity to combat climate change. We suggest a novel method of spatial planning that enhances windfarm sustainability: investments are prioritized in the most fragmented zones that lie outside the Natura 2000 network of protected areas. We showcase it in Greece, a biodiversity hotspot with a strong climate policy and land conflict between conservation and wind energy schemes. The analysis indicates that the suggested investment zone supports wind harnessing 1.5 times higher than the 2030 national goal, having only marginally lower (4%) wind speed. It performs well for the conservation of the annexed habitats and species of the two Nature Directives and it greatly overlaps with the Important Bird Areas (93%) and the roadless areas (80%) of Greece. It also greatly overlaps (82%–91%) with the exclusion zones suggested according to three sensitivity maps for bird conservation. Since land use change triggers biodiversity decline, we underline the necessity of such approaches for meeting both climate and biodiversity goals and call for a greater environmental policy convergence towards biodiversity conservation and no net land take. Display omitted •A paradox of impacting on biodiversity to combat climate change emerges.•Sustainable scenario: locate windfarms in fragmented land outside protected areas.•The scenario hampers fragmentation and benefits biodiversity in Greece.•The scenario meets climate goals for 2030 and beyond.•Need for environmental policy towards the no net land take milestone.