Chitosan (C) is a natural antimicrobial compound that has been widely explored for wood protection, but its application is limited by its high leachability. Genipin is a biobased crosslinking agent that can crosslink with chitosan under mild conditions. This study aims at examining the decay resistance and leachability of genipin-crosslinked chitosan (GC) treated wood against common wood-decaying fungi. GC formation was confirmed using Fourier transform infrared spectroscopy and Thermogravimetric analysis. The antifungal efficacy of GC against two brown-rot fungi, Gloeophyllum trabeum (G.t.) and Rhodonia placenta (R.p.) and two white-rot fungi, Trametes versicolor (T.v.) and Irpex lacteus (I.l.) was first determined using malt-gar as substrate, which revealed that GC exhibited similar efficacy as C treatments in inhibiting the growth of all fungi studied. Micrographs of light and fluorescence microscopy showed changes in fungi morphology and nuclei deformation due to the effect of GC. GC-treated wood samples show an increased retention and mass gain as the function of treating concentrations, which were as high as 21 kg/m2 and 3.6%, respectively. However, upon leaching test, the mass gain of 3% GC treated softwood and hardwood was reduced to 1.6% and 0.9%, respectively, indicating cross-linking chitosan with genipin did not reduce the leaching rate of chitosan. In terms of durability testing, GC treated wood samples showed significantly lower mass loss ranging from 11 to 15% than those of the control groups of ≥30% regardless of the leaching test. •Chitosan can crosslink with genipin with improved thermal stability.•Genipin crosslinked chitosan has similar antifungal properties against common wood decaying fungi.•Genipin crosslinked chitosan treatment caused morphological changes and nuclei deformation of all the tested fungi.•Genipin crosslinked chitosan treated wood has limited improved leachability.