Research has demonstrated that intraspecific functional trait variation underpins plant responses to environmental variability. However, few studies have evaluated how trait variation shifts in response to plant pathogens, even though pathogens are a major driver of plant demography and diversity, and despite evidence of plants expressing distinct strategies in response to pathogen pressures. Understanding trait-pathogen relationships can provide a more realistic understanding of global patterns of functional trait variation. We examined leaf intraspecific trait variability (ITV) in response to foliar disease severity, using Coffea arabica cv. Caturra as a model species. We quantified coffee leaf rust (CLR) severity—a fungal disease prominent in coffee systems—and measured key coffee leaf functional traits under contrasting, but widespread, management conditions in an agroforestry system. We found that coffee plants express significant ITV, which is largely related to shade tree treatment and leaf position within coffee canopy strata. Yet within a single plant canopy stratum, CLR severity increased with increasing resource conserving trait values. However, coffee leaves with visible signs of disease expressed overall greater resource acquiring trait values, as compared to plants without visible signs of disease. We provide among the first evidence that leaf traits are correlated with foliar disease severity in coffee, and that functional trait relationships and syndromes shift in response to increased disease prevalence in this plant-pathogen system. In doing so, we address a vital gap in our understanding of global patterns of functional trait variation and highlight the need to further explore the potential role of pathogens within established global trait relationships and spectra.