Due to rising environmental concerns and the necessity to reduce the use of fossil-based resources, the development of fully/partially bio-based polymer composites have gained considerable attention. In this connection, an attempt has been made to develop partially bio-based vanillin-based polybenzoxazine-silica (PBZ-Si) hybrid nanocomposites by simple sol–gel approach for multifunctional applications, including oil–water/ oil–water emulsion separation, anti-icing, thermal, and corrosion resistance. The benzoxazine monomers (V-fa and V-sa) were prepared through Mannich reaction using vanillin (V), stearylamine (sa)/ or furfuryl amine (fa) and paraformaldehyde. The synthesized benzoxazines were confirmed by FT-IR, 1H NMR, and DSC. To enhance the hydrophobic, and thermal properties of the neat PBZ, silica was introduced to develop PBZ-Si hybrids by an in-situ sol–gel approach using V-fa/ or V-sa, 3-aminopropyl triethoxysilane (3-APTES) and tetraethyl orthosilicate (TEOS) followed by thermal ring-opening polymerization. The incorporation of silica into PBZ hybrid composites enhanced the thermal stability, good oil–water/ oil–water emulsion separation and anti-corrosion properties. Notably, the PBZ-Si hybrid composites coated cellulose substrate showed a higher value of water contact angle of 156 ± 1° and achieved a high oil flux value of 27,283 Lm−2 h−1 and separation efficiency of 99.5% even after 20 cycles. The PBZ hybrid coated on cellulose substrate exhibited better separation ability even after the substrate was treated with adverse conditions, including acidic, basic, abrasion, and temperature. Further, the PBZ-Si hybrids coated on MS substrates revealed good corrosion-resistant behaviour with an inhibition efficiency of 96%. As research and development continue, these bio-based, sustainable PBZ hybrid materials may play a pivotal role in advancing separation technologies and corrosion-resistant applications.