Avian mortality is one of the most negative impacts of wind energy. Consequently, techniques that effectively reduce avian collision rates are necessary. One of such method is the stop-turbine system, otherwise known as a Turbine Shutdown System (TSS). Here, we analyzed changes in mortality during 15 years, starting two years before the application of a selective stopping protocol (2006–2007) and after 13 years of application (2008–2020). This protocol was applied in Cadiz area (southern Spain) to 20 wind farms, totaling 269 wind turbines. The priority in the shutdown protocol was to avoid large soaring birds, mainly raptors, collisions. In total, 2903 birds and 354 bats were found to have collided with wind turbines in this 15-year period. This represents a rate of 0.830 birds/turbine/year and 0.101 bats/turbine/year. After implementation of the selective stopping protocol, we found a significant reduction of 61.7 % in mortality of soaring birds (mainly raptors and storks). Considering only mortality records of Griffon Vultures, a reduction of 92.8 % was achieved. Counts of Griffon Vultures increased more than 7-fold during the study period, and number of turbine stops due to vultures at risk in wind farms, also increased by around 2.5 times. Our finding of Griffon Vulture mortality being reduced by over 92 % through turbine shutdowns was associated with only an estimated loss of less than 0.51 % in energy production. This substantial disparity in conservation benefits versus industrial costs suggests that this mitigation method could have net-beneficial application elsewhere.