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Biological control agents (BCAs) are reported to control plant diseases by directly targeting pathogens or indirectly by enhancing the plant's immune system. It has also been reported that plants exhibit genetic variation for compatibility with BCAs, ultimately impacting biocontrol efficacy. This study explored transcriptomic host responses of two winter wheat genotypes differing for biocontrol efficacy of the fungal BCA C. rosea in controlling septoria tritici blotch disease caused by the fungus Zymoseptoria tritici . Leaves of winter wheat genotypes NGB6704 (high biocontrol efficacy) and NGB348 (low biocontrol efficacy) were spray inoculated with C. rosea , Z. tritici, or their co-inoculation and were harvested at 8 h, 16 h, 32 h, and 40 h for differential gene expression analysis. The results indicate genotype-dependent and time-dependent responses in gene expression towards C. rosea and Z. tritici . Induction of several defense-related genes associated with pattern-triggered immunity and effector-triggered immunity was also observed in interactions with C. rosea exclusively and in the presence of Z. tritici . NGB348 showed a stronger expression of defense-related genes when inoculated with C. rosea at early time points, while NGB6704 exhibited a stronger response at 40 h, emphasizing the differential responses to the presence of C. rosea by the two genotypes, ultimately affecting STB disease development. Cross-referencing differentially expressed genes with genes segregating for C. rosea biocontrol efficacy identified genes associated with receptor-like protein kinases, chitinases, oxalate oxidases, and E3 ubiquitin-protein ligases. Further microscopic and functional validation studies are recommended to determine the intricate nature of plant genotype-specific interactions.