In the last century climate change has been a major threat to biodiversity, ecosystem services, and human well‐being. Atmospheric oscillations that occur at the regional oceanic flow pattern may affect significantly the climate of the Earth. In this study, we investigate the effects of ENSO (El Nino Southern Oscillation) and NAO (North Atlantic Oscillation) on the Mediterranean crop yield using the Nino 3, Nino3.4, Nino 4, ONI and NAO indices. Olive, which is a bioindicator type in the Mediterranean, and cotton and grapes with high yield and economic value crops were examined. According to the average production amounts in the Mediterranean Region between 1991 and 2020, 39% of cotton production is in Adana (205319 tone), 43% of grape production is in Mersin (228471 tone) and 37% of olive production is in Hatay (103854 tone). As a method, firstly, Mann Kendall rank correlation test was applied to the yield values of the crops. After the 2000s, it has been determined that the trend of yield has changed and was obtained an increasing trend. Secondly, the correlation between the yields and Nino 3, Nino3.4, Nino 4, and NAO indices were determined with the Spearman correlation coefficient. Accordingly, a high correlation of 50% and 80% was found at the p ≤ 0.05 and p ≤ 0.00 significance level in the phenological periods of the crops. The highest correlations were determined especially during the flowering period (April, May, June) for olive and grape yield with El Nino indices. The frequency of the correlation detected with the NAO index is weak. The effect on the efficiency of the phases when El Nino indices are strong was examined graphically. Accordingly, in the 1997 and 2015-2016 periods, when the El Nino phenomen was very strong, there were sharp decreases in the crop yields. This variability affects the countries whose economic activity is based on agriculture in the Mediterranean Basin, and it is likely to affect the food industry in the future.