In the present study, biogenic silica nanoparticles (bSNPs) were synthesized from groundnut shells and thoroughly characterized to understand its phase and microstructure properties. The biopolymer was synthesized from yeast Wickerhamomyces anomalus and identified as Poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) by GC-MS and NMR analysis. The bSNPs were reinforced to fabricate PHBV/SiO2 nanocomposites via solution casting technique. The fabricated PHBV/SiO2 nanocomposites revealed intercalated hybrid interaction between the bSNPs and PHBV matrix through XRD analysis. PHBV/SiO2 nanocomposites showed significant improvement in physical, chemical, thermo-mechanical and biodegradation properties as compared to the bare PHBV. The cell viability study revealed excellent biocompatibility against L929 mouse fibroblast cells. The antibacterial activity of PHBV/SiO2 nanocomposites was found to be progressively improved upon increasing bSNPs concentration against E. coli and S. aureus.