Wildlife have become increasingly dependent on anthropogenic resources, altering interactions between individuals and subsequently disease transmission. Further, nutritional quantity and quality impact an individual's ability to mitigate damage caused by infectious disease. Thus, understanding how diet affects immune function is critical for predicting disease severity and transmission. Here, we use transcriptomics to explore the previously unstudied molecular mechanisms underpinning diet-driven differences in pathogen tolerance. Using a widespread avian bacterial pathogen, we find significant diet-driven differences in the expression of many genes encoding immune response and translational machinery proteins. Prior to infection, protein-fed birds are more transcriptionally primed for infection than lipid-fed birds, resulting in greater tolerance for protein-fed birds during the recovery period. Given the importance of human supplemented food in wildlife disease systems, the molecular mechanisms by which interactions between diet and infection emerge provide insight into the ecological and immunological consequences of human behaviour on wildlife disease.