Wind is increasingly being used as a renewable energy source around the world. Avian mortality is one of the negative impacts of wind energy and a new technique that reduces avian collision rates is necessary. Using the most frequently-killed species, the griffon vulture (Gyps fulvus), we studied its mortality at 13 wind farms in Tarifa, Cadiz, Spain, before (2006–2007) and after (2008–2009) when selective turbine stopping programs were implemented as a mitigation measure. Ten wind farms (total of 244 turbines) were selectively stopped and three wind farms (total of 52 turbines) were not. We found 221 dead griffon vultures during the entire study and the mortality rate was statistically different per turbine and year among wind farms. During 2006–2007, 135 griffon vultures were found dead and the spatial distribution of mortality was not uniformly distributed among turbines, with very few turbines showing the highest mortality rates. The 10 most dangerous turbines were distributed among six different wind farms. Most of the mortalities were concentrated in October and November matching the migratory period. During 2008–2009, we used a selective stopping program to stop turbines when vultures were observed near them and the griffon vulture mortality rate was reduced by 50% with a consequent reduction in total energy production of by the wind farms by only 0.07% per year. Our results indicate that the use of selective stopping techniques at turbines with the highest mortality rates can help to mitigate the impacts of wind farms on birds with a minimal effect on energy production.