Intercropping a grain legume with a grain nonlegume is of increased interest by producers in the Canadian Prairies, especially under organic production where intercropping is an alternative to the lack of economic returns of green manure or summer fallow. Information on the impacts of intercropping on root rot, a significant challenge for legume crops, is needed. The objective of this organic study, conducted over 2 years (2017-2018) in the semiarid Canadian Prairies, was to determine how intercrops of lentil (Lens culinaris Medik.)-yellow mustard (Sinapis alba L.) and field pea (Pisum sativum L.)-oat (Avena sativa L.), at different seeding ratios, might affect in-season root rot development and associated fungal communities. This 2-year study showed that the impacts of intercropping varied between crop combinations and among fungal species. Multiple pathogens, as well as saprophytes, were associated with the intercrops and respective monocultures, with most being Fusarium species. For intercropped lentil, there was a >50% reduction in the mean root rot severity, and an 11% reduction in the isolation of total Fusarium species, compared to its monoculture. These results suggest disease suppression in the intercropped lentil, which might be attributed to allelopathy from mustard leading to an increase in fungi with biocontrol potential (antagonists). These antagonist fungi were 84% higher in lentil intercropped with a full mustard ratio than in its monoculture. In contrast, root rot in pea intercropped with oat was mostly higher than in the pea monoculture, attributed to the prevalence of similar species, including Fusarium pathogens, common to both crop species.