Imbalanced nutrition has a major impact on crop productivity, particularly in hyper-arid environments, and precise interpretation is essential for designing appropriate nutrient management strategies. Compositional nutrient diagnosis (CND) was used to identify nutritional imbalances of multiple nutrients (N, P, K, Ca, Mg, Fe, Mn, Zn, and Cu) in wheat and faba bean cultivated in Kharga Oasis, Egypt. Significant nutrient interactions were also assessed using principal component analysis. Due to large differences in water and soil characteristics, wheat and faba bean yields from the surveyed area varied greatly, ranging from 2118 to 8211 and 1373 to 4962 kg ha-1, respectively. The CND indexes for the low-yield subpopulation of wheat were negative for P, Ca, and Zn, with average values of -0.82, -2.66, and -1.26, but positive for K, Mg, Fe, and Mn with average values of 4.80, 4.92, 1.70, and 0.57, respectively. In faba bean, N, P, Ca, and Zn were negative, with average values of -1.73, -0.67, -8.19, and -1.41, but K, Mg, Fe, Mn, and Cu were positive with average values of 2.62, 0.50, 1.32, 1.10, and 0.40, respectively. Synergistic interactions P-Zn and Mg-Fe, as well as antagonistic interactions P-Mg, P-Fe, Zn-Fe, Zn-Mg, Ca-Cu, N-Mn, Mn-Cu, and P-Ca, were evident from the principal component analysis of the data. This investigation reveals that the decline in crop yields in the study area is due to nutritional imbalance induced by a deficiency of Ca, Zn, and P and a surplus of Mg, K, Fe, and Mn, in addition to nutrient antagonism.