A method to improve wood durability using natural extracts was evaluated. Wood deterioration is a condition caused by several abiotic and biotic factors including fungal contamination. To date, approaches aiming at the reduction of these contaminants mainly involve the use of chemicals agents. Natural products could represent an alternative strategy. Aqueous extracts of Punica granatum L. (pomegranate) peel and Melia azedarach L. barks were evaluated as antifungal agents to improve natural durability of beech wood and maritime pine. To evaluate the effect of treatments under simulated accelerated ageing of wood by natural conditions, impregnation and leaching tests were performed. Results demonstrated that samples impregnated with pomegranate or M. azedarach solutions notably increased the biological resistance of wood in a dose-dependent manner. These results were confirmed by the reduction in weight losses in treated samples even after 6 weeks of fungal exposure. Moreover, after leaching tests, 20 and 7% (w/v) of pomegranate and M. azedarach extract solutions were demonstrated as the better concentrations to enhance wood durability. Total phenol content and characterization of the phenolic compounds in both, natural extracts and wood samples were analyzed by Folin–Ciocalteu assay and HPLC-DAD. In conclusion, it was demonstrated that the present method can be considered as an effective treatment to increase wood durability while it proposes the valorization of natural extractives in wood industry.