Widespread usage of intercropping systems has been limited because of a lack of knowledge about the key factors that affect the performance of intercrop components. We used general linear modelling to explain the effect of different cropping systems on the relationships among yield, thousand kernel weight (TKW), and crude protein of cereal crops under the same agro-ecological conditions and naturally occurring inocula of obligate pathogens. The results of our study showed that the yield variation under extreme fluctuations in climatic conditions could be lowered through intercropping cultivation. The disease indices of leaf rust and powdery mildew were highly dependent on the type of cultivation. The relationships among the levels of pathogenic infection and yield performances were not straightforward and were highly dependent on the yielding potentials of the cultivars. Our study indicated that changes in yield, TKW, and crude protein, as well as their relationships during intercropping cultivation, were cultivar specific and, therefore, not the same among all cereal crops exposed to the same agro-ecological conditions.