Aims <p>Intercropping is gaining increasing attention as a way towards developing sustainable agriculture. Positive effects on yield and biodiversity have been reported, but the effects of intercropping on soil-borne pathogen pressure are still underexplored.</p> Methods <p>Therefore, we performed a plant-soil feedback (PSF) experiment with oat on soils originating from oat monocultures and the middle and the edge of oat strips intercropped with cabbage. Using amplicon sequencing, we determined the relative abundance of soil-borne fungi in soils and roots to link PSF effects to fungal pathogen communities.</p> Results <p>Oat experienced negative PSF on all soils, but surprisingly, the effect was most negative in the edge of oat strips. This negative PSF coincided with an increase in the relative abundance of oat-specific fungal pathogens in oat roots, but also with reduced availability of soil nutrients.</p> Conclusions <p>Our study on oat does not support the idea that intercropping can contribute to mitigating effects of negative PSF – especially not in the edges of the strips. The negative PSF was related to an increased abundance of host-specific pathogens, but also to reduced nutrient availability. Understanding how intercropping affects negative PSF requires integrating interactions between host-specific pathogens and soil nutrient availability.</p>