Abstract Within-host spread of pathogens is an important process for the study of plant-pathogen interactions. However, the development of plant-pathogen lesions remains practically difficult to characterize beyond the common traits such as lesion area. Here, we address this question by combining image-based phenotyping with mathematical modelling. We consider the spread of Peyronellaea pinodes on pea stipules that were monitored daily with visible imaging. We assume that pathogen propagation on host-tissues can be described by the Fisher-KPP model where lesion spread depends on both a logistic growth and an homogeneous diffusion. Model parameters are estimated using a variational data assimilation approach on sets of registered images. This modelling framework is used to compare the spread of an aggressive isolate on two pea cultivars with contrasted levels of partial resistance. We show that the expected slower spread on the most resistant cultivar is actually due to a decrease of diffusion and, to a lesser extent, growth rate. These results demonstrate that spatial models with imaging allows one to disentangle the processes involved in host-pathogen interactions. Hence, promoting model-based phenotyping of interactions would allow a better identification of quantitative traits thereafter used in genetics and ecological studies.