The suppressive influence of compost towards the soil-borne fungus Fusarium oxysporum f. sp. lycopersici on tomatoes with special emphasis on root morphological modifications was examined. Roots of inoculated and non-inoculated tomato plants, grown in three different substrates (control, 20 % compost and 40 % compost), were scanned and analyzed in order to identify their morphological traits. To examine a potential systemic effect of compost, the plants were placed in individual pots or in split-root systems. Obtained results showed that F. oxysporum f. sp. lycopersici caused decreased root lengths and reduced root weight, root surface area and root volume. Furthermore, an increase in fine root fraction and specific root length was observed in inoculated plants. Substrate containing 20 % compost had a clear stabilizing effect towards pathogenrelated changes of the root morphology and was best able to mitigate below-ground symptoms on plants cultivated in individual pots. The morphology of roots grown in split-root systems was not directly affected by the presence of F. oxysporum f. sp. lycopersici, but complex interactions between the pathogen and the substrate were observed, strongly depending on which substrate was inoculated. These results indicated that soil amendment with compost in moderate amounts contributes to plant health and could provide an alternative to peat based substrates in sustainable production systems.