To obtain further insight into the intricate inter-play between maize (Zea mays) and the fungal pathogen Colletotrichum graminicola, the local and systemic molecular and chemical defence responses of maize leaves and roots were simultaneously investigated and compared. Similar gene expression and hormonal patterns were detected in both above- and below-ground organs; however, roots responded more rapidly and accumulated higher levels of defence-related hormones than leaves. Leaf and root infection with C. graminicola triggered systemic resistance in the foliage against the same fungus. This systemic defence response was associated with systemic transcriptional adaptations, and elevated levels of salicylic acid and abscisic acid. Metabolomic profiling revealed significant differences in the composition of secondary metabolites in leaves and roots, indicating that these organs employ distinct chemical defence systems. In addition, higher basal levels of antimicrobial flavonoids suggest an enhanced basal defensive state of roots. Our findings reveal tissue-specific local and systemic antifungal defence mechanisms in maize.