Wind energy is considered a clean energy source, but produces negative impacts regarding avian mortality. The Barão de São João wind farm in Portugal’s Sagres region is part of an important migratory flyway, crossed by 5000 individuals of 30 soaring bird species every autumn. The wind farm’s licensing was conditioned to the implementation of rigorous mitigation procedures, namely a Radar Assisted Shutdown on Demand (RASOD) protocol to reduce the probability of bird casualties. A security perimeter with observers was aided by a radar system, detecting soaring birds approaching the wind farm. Turbines were to be turned-off when pre-defined criteria of intense migration or presence of threatened species were met. Turbine shutdown was operated by the wind farm staff after a request from the monitoring team (MT), or directly by the MT. Of the soaring birds crossing the wind farm, 55% were recorded at altitudes associated with high collision risk. However, due to RASOD, no soaring birds died from collisions during five consecutive autumns. The average annual shutdown period decreased continuously after the first year (105 h) reaching only 15 h when the MT was given direct access to shut down operations through SCADA (the remote system to monitor and control wind turbines). Shutdown period corresponded only to 0.2–1.2% of the equivalent hours in a year’s wind farm activity. The use of radar, direct access to SCADA and cumulative experience by the MT improved the procedure’s efficiency, allowing better judgments on the application of shutdown orders. Our results indicate that RASOD may be an essential tool in reconciling wind energy production with the conservation of soaring birds.