Bio-based materials, such as wood bio-concrete (WBC), hold promise in reducing energy consumption and carbon footprint of the construction industry. However, the durability of these materials is not well understood and can be negatively affected by the high water absorption capacity of wood bio-aggregates. In the field of cement composites, for example, silane-siloxane-based water repellent has been used to protect such materials from natural environmental attack. Nevertheless, there is still a limited understanding of various aspects related to this type of treatment, including its performance when applied to the bio-concrete substrate. This research aimed to investigate the influence of silane-siloxane on the rheology and hydration of cementitious paste through isothermal calorimetry and thermogravimetric analysis. Additionally, the impact of silane-siloxane on the physical and mechanical properties of WBCs was examined by conducting tests at fresh state (flow table and entrained air content) and hardened state (compressive strength and capillary water absorption). The composites were produced with a volumetric fraction of 45% of wood shavings while the cement matrix consisted of a combination of cement, rice husk ash, and fly ash. Silane-siloxane was applied in three ways: as coating, incorporated as an admixture, and in a combination of both methods. The results indicated that by incorporating silane in the cementitious pastethe viscosity increased by 40% and the hydration was delayed by approximately 6 h when compared to the reference. In addition, silane improved the compressive strength of WBCs by 24% when incorporated into the mixture, expressively reduced the water sorptivity of WBCs (93%), and was more effective if used as coating.