Banana (Musa spp.) is essential for food security. For its clonality is highly susceptible to pests and diseases. The wilt fungus Fusarium oxysporum f. sp. cubense Tropical Race 4 (FocTR4) threatens banana production worldwide. We notice that chitosan protects banana from biotic stress. Chitosan, a plant defence elicitor with antimicrobial activity, triggers salicylic acid (SA) and methyl salicylate biosynthesis and induces systemic acquired resistance (SAR) genes, mainly flavin-dependent monooxygenase 1 (FMO1), in banana. Chitosan promotes root exudation of SA and emission of methyl salicylate (MeSA). Banana germplasm, Petit Naine, Gros Michel, Enzirabahima, Yangambi Km5 and Foconah banana differ in their response to chitosan. Chitosan induces, in Foc resistant Yangambi Km5, ca. 7-fold FMO1. Preventive chitosan treatments together with the endophytic biocontrol fungus Pochonia chlamydosporia strain 123 reduce (ca. 4-fold) colonization of banana roots by FocTR4. Therefore, chitosan and beneficial endophytes can help to manage sustainably FocTR4 in banana.