We propose a methodology to estimate the yield response factor (i.e., the slope of the water-yield function) under local conditions for a given crop, weather, sowing date, and management at each growth stage using AquaCrop-OS. The methodology was applied to three crops (maize, sugar beet, and wheat) and four soil types (clay loam, loam, silty clay loam, and silty loam), considering three levels of bulk density: low, medium, and high. Yields are estimated for different weather and management scenarios using a problem-specific algorithm for optimal irrigation scheduling with limited water supply (GET-OPTIS). Our results show a good agreement between benchmarking (mathematical approach) and benchmark (estimated by AquaCrop-OS) using the Normalised Root Mean Square Error (NRMSE), allowing us to estimate reliable yield response factors ( K y ) under local conditions and to dispose of the typical simple mathematical approach, which estimates the yield reduction as a result of water scarcity at each growth stage.