Seed plants are regularly exposed to pathogenic microbes yet do not always display disease symptoms. Here, Hiruma et al. carried out a detailed characterisation of the root-colonizing endophytic fungus Colletotrichum fructicola (CfE) and a closely related pathogen, C. gloeosporioides (CgP), identified in asymptomatic field-grown Brassicaceae plants to understand the role played by beneficial microbes in this process. They found that CfE suppresses pathogenic fungal growth possibly through the production of antifungal metabolites, while endophytic colonization of CfE and its host-protective function depends on host-derived tryptophan-based antimicrobial metabolites. These findings highlight how fungus–fungus competition is managed by the host to avoid disease progression. See also Commentary by Wang, in this issue.