Wood, a vital material for both modern and heritage objects, is particularly susceptible to degradation caused by water due to its hydrophilic nature and porous structure. Therefore, developing sustainable strategies to protect wood is of significant importance. This study aims to produce a highly hydrophobic coating for the protection of wood following a straightforward procedure and using materials that are compatible with wood. First, nano/sub-microlignin (NL) is isolated and produced from beech wood through a one-step tailored organosolv process. Next, NL is incorporated into Sivo 121, a water-borne and solvent-free silane system recommended by the manufacturer for protecting wood surfaces. Composite coatings containing various concentrations of NL and Sivo 121 are applied to chestnut (Castanea spp.) and oak (Quercus spp.). The impact of NL concentration on the contact angles of water drops (CAs) and colour changes (ΔE) of the treated wood specimens is investigated. The coating with 4% w/w NL demonstrates enhanced hydrophobicity (CA = 145°) and has a negligible effect on the colour of pristine oak (ΔE < 3). The wetting properties of coated oak are not affected after 100 tape peeling cycles. However, the coating exhibits poorer performance on chestnut, i.e., CA = 135°, which declines after 80 peeling cycles, and ΔE > 5. The drop pH does not have any noticeable effect on CA. The latter remains stable even after prolonged exposure of coated oak and chestnut samples to artificial UV radiation and outdoor environmental conditions. Finally, the composite coating offers good and comparable protection for both wood species in the biological durability soil burial test