Wind energy has great potential to drive Chile's energy sector towards a more sustainable model; however, it could induce landscape changes impacting ecosystem services. Accordingly, this study aimed to identify the best areas for wind energy development in Biobío and Ñuble regions, by integrating metrics from suitability analysis, ecosystem service valuation and exergy. The trade-offs between ecosystem services and wind electricity generation were assessed through biophysical indicators. Then, a new indicator based on ecosystem services impacts and exergy concept was developed to determine the most sustainable sites for wind energy development. Results showed that deploying wind energy could have the highest adverse effects on erosion regulation services, with an increase of 40%–50% in soil loss for Ñuble and Biobío. Moreover, the crop and timber provision were also reduced by 10%, while water-related services were favored by an increment of 10% in water savings. The proposed indicator took negative values in all suitable zones under analysis (−25 to −307 GJex/GWh), indicating that ecosystem services losses exceeded gains. Results suggest that seven zones are potential sites for wind energy development based on their impacts which were up to −39 GJex/GWh. This work provides evidence for promoting sustainable wind energy planning by locating the projects in zones with the lowest detrimental ecosystem services impacts.