Perennial grain crops are emerging as a promising addition to sustainable agricultural systems because of their low-input requirements and delivery of ecosystem services. However, adoption of these crops is expected to bring novel management challenges, including those related to plant diseases. In New York, fungal pathogens of annual grains have a significant impact on crop yield and value and are generally controlled through a combination of host resistances, cultural practices and chemical fungicides. Without the availability of crop rotation and soil tillage practices, disease control in perennial grain systems may be problematic, and little is known about perennial grain crop susceptibility to local plant pathogen populations. During 2017 and 2018, ongoing field trials of two perennial grain crops recently introduced in New York, intermediate wheatgrass (IWG; Thinopyrum intermedium) and perennial cereal rye (PCR; Secale cereale), were assessed for the presence of putative fungal pathogens on actively growing plants, overwintered crop residue and harvested grain. A total of nine potential host–pathogen combinations were recorded based on symptomology, pathogen morphology and DNA sequences. Common annual crop pathogens were recovered most frequently, but, at one site, Phyllachora graminis, causal fungus of tar spot and a pathogen not previously reported on crops in New York, was found on IWG. Residue colonization by an important toxigenic pathogen (Fusarium graminearum) was high in both crops, though mycotoxin levels in associated grain were low, indicating either the hosts or environment were unsuitable for disease development. Seed-borne fungal communities differed across crops and locations, and black point, a condition caused by Alternaria and Bipolaris fungi and indicative of compromised grain quality, was prevalent in PCR under some conditions. Growing PCR with intercropped red clover (Trifolium pratense L.) resulted in less Stagonospora colonization of stem residue, and PCR grown with an oat (Avena sativa L.) nurse crop had a reduced incidence of black point. These alternative cultural practices may prove useful for managing disease in perennial grains. Our results suggest that the incorporation of perennial crops into the agricultural landscape will lead to familiar plant disease problems requiring new solutions as well as new problems that may require significant research investments.