Climate change is a major threat to the survival of our natural ecosystems by altering environmental conditions, presenting a One Health challenge with severe consequences on human and animal health, access to resources, and global food security and safety. Many climatic change effects on crops are exasperated by the increased prevalence of fungal diseases, including the emergence of new species and strains with increased dispersal and virulence that can spread to new geographical and host ranges. For the globally devastating fungal disease of cereal crops, Fusarium head blight (FHB), infection reduces crop yields and quality while contaminating food products with mycotoxins, such as deoxynivalenol (DON). Our research uses state-of-the-art mass spectrometry-based proteomics combined with tandem mass tag labeling to define temporal and resistance-specific host-pathogen interactions between the pathogen (Fusarium graminearum) and the host (Triticum aestivum). We profiled core proteome defense responses independent of cultivar but regulated across time (24 vs. 120 h post inoculation), along with cultivar-specific responses to infection. Comparison of in vitro fungal proteome vs. infectome profiling, revealed uncharacterized fungal proteins with altered abundance profiles dependent upon disease progression. Moreover, emphasis on the host response to infection revealed common signatures of defense responses and energy redistribution to protective mechanisms within the FHB-resistant variety that remained unchanged in susceptible wheat. Overall, our study aims to enhance effectiveness of cultivar resistance, reduce severity of infection, and increase strategies to prevent fungal disease in cereal crops for improved global food security and safety.