Enhanced understanding of the climate impact on crops' production is necessary to cope with expected climate variability and change. This study was conducted to find any robust association between crop yield and evapotranspiration using historical data (1986–2005) and subsequently employ the acquired relationship to project crop yield under future climate conditions for two agricultural centers in northeast Iran. Three legume crops of chickpea, lentil, and bean were selected in this study. The future precipitation and temperature data were projected by downscaling outputs of global climate model HadCM3 (A2 scenario) by LARS-WG stochastic weather generator. The data were downscaled for the baseline (1961–1990) and two time periods (2011–2030 and 2080–2099) as near and far future conditions. Projected temperature under A2 scenario showed increasing trend changed from 4 to 26% during the legumes' growth period compared to baseline. In addition, projected annual precipitation change was between −14 and 10% range under different time periods in contrast to baseline. There was a nonlinear relationship between crop yields and the seasonal values of crop evapotranspiration for all crops. The results showed that seasonal evapotranspiration would increase under climate change conditions across study locations. Crop yield would also increase for chickpea but not for lentil and bean for the far future in Sabzevar location compared to baseline. In conclusion, increasing the temperature and decreasing the precipitation may have a negative effect on legumes' yield in northeast Iran, especially for far future conditions. Therefore, planning effective adaptation and mitigation strategies would be necessary for northeast Iran.