We have well-established techniques to visualise the movement of a fungal pathogen within plant tissues. We also have improved our ability to characterise host resistance and susceptibility genes that are key to disease resistance. However, we are still building the foundation knowledge to define the spatially resolved molecular interactions between host and pathogen, the impact on plant physiology at the point of infection, tissue recovery post-disease disruption, and the plant’s ability to tolerate disease pressure. To address this, we are applying phenotyping, “omic” and novel data analytic approaches to resolve complex traits, such as disease tolerance. Continued exploration of the physiological responses in infected crops aims to unlock new knowledge for breeders to develop crops with increased performance.