Intercropping is a sustainable practice becoming increasingly popular in the Canadian Prairies. However, its long-term impact on diseases in subsequent sole crops is not well understood. We examined root rot and associated fungal communities in durum wheat [Triticum turgidum L. ssp. durum (Desf.) Husn.], following different ratios of lentil (Lens culinaris Medik.)-yellow mustard (Sinapis alba L.), and field pea (Pisum sativum L.)-oat (Avena sativa L.) intercrops, and respective monocultures, in a semiarid region of the Canadian Prairies (2018-2019). The previous crop(s) impacted disease severity in durum wheat and had a significant impact on the composition of fungal communities. Durum grown after the mustard monoculture and its high-ratio intercrop had 15% less severe root rot than after the lentil monoculture and its high-ratio intercrop, while durum following the oat monoculture and its intercrops had 16% more severe root rot than after mustard and its intercrops. Fusarium species were the most frequent fungal isolates, accounting for 70% of total isolations. The main Fusarium cereal pathogens were >1.7x-25.5x higher following the oat than the mustard monoculture and 2x-3x higher after the pea-oat than the lentil-mustard intercrops. In turn, isolation of the main fungi with biocontrol potential (antagonists) was 4.3x-5x higher after the mustard than oat monoculture, and 2x higher after lentil-mustard than pea-oat. The prevalence of antagonists in mustard-containing treatments, and their negative correlation with disease levels, suggest a dual mechanism of disease suppression: a direct pathogen inhibition through the mustard's allelopathy and enhanced populations of indigenous microbial antagonists.