There has been a growing interest in seeking natural and biobased preservatives to prevent the wood from deteriorating during its service life, thereby prolonging carbon storage in buildings. This study aims to assess the in vitro and in vivo antifungal properties of epsilon poly-L-lysine (EPL), a secondary metabolite from Actinomyces, against four common wood-inhabiting fungi, including two brown-rot fungi, Gloeophyllum trabeum (GT) and Rhodonia placenta (RP), and two white-rot fungi, Trametes versicolor (TV) and Irpex lacteus (IL), which has rarely been reported. Our results indicate that these fungi responded differently due to EPL treatment. From the in vitro study, the minimal inhibitory concentration of EPL against GT, TV, and IL was determined to be 3 mg/ml, while that of RP was 5 mg/ml. EPL treatment also affects the morphology of fungal hyphae, changing from a smooth surface with a tubular structure to twisted and deformed shapes. Upon EPL treatment with wood samples (in vivo), it was found that EPL could possibly form hydrogen bonds with the hydroxy groups in wood and was uniformly distributed across the transverse section of the wood samples, as indicated by Fourier transform infrared spectroscopy and fluorescence microscopy analyses, respectively. Compared with control wood samples with a mass loss of over 15% across different fungi, wood samples treated with 1% EPL showed negligible or very low (<8%) mass loss. In addition, the thermal stability of EPL-treated wood was also improved by 50%. This study suggests that EPL could be a promising alternative to traditional metallic-based wood preservatives.