Canopy-level interactions have been largely ignored in epidemiological models and their applications in defining disease risks under climate change, although these interactions are important for disease management. This paper uses anthracnose of Stylosanthes scabra as a case study and reviews research on dynamics of the pathogen (Colletotrichum gloeosporioides) at the canopy level and pathogen evolution under changing climate. It argues that linking of pathogen dynamics, crop growth and climate models is essential in predicting disease risks under climate change. A plant functional-structural model was used to couple S. scabra growth and architecture with disease under ambient and elevated CO2. A level of induced resistance in plants with enlarged canopy determined anthracnose severity at elevated CO2. Moisture-related microclimatic variables determined infection at ambient but not at elevated CO2. At high CO2 increased disease level from raised pathogen fecundity in enlarged canopy accelerated pathogen evolution after 25 sequential infection cycles. Modelling of pathogen dynamics under climate change currently suffers from a paucity of quantitative data, mismatch of scales in coupling climate and disease models, and model uncertainties. Further experimental research on interactions of biotic and abiotic factors on plant diseases under climate change and validation of models are essential prior to their use in climate-change prediction. Understanding and anticipating trends in host–pathogen evolution under climate change will improve the durability of resistance and lay the foundation for increased crop adaptation through pre-emptive plant breeding.