In concrete industry, geopolymer acts as an alternative building material of ordinary cement and possess similar/greater mechanical strength and durability, fashioned by industrial by-product; fly ash with alkaline activator. Accompanied by the chemical corrosion, biogenic corrosion is a foremost obstruction in sewer systems, bridge piers, pipelines and offshore platforms. The present works has been given an effort to introduce an anti-bio deteriorate sustainable geopolymer (GMZnO–Si) through the decoration of spherical nano silica (Si) on zinc oxide Nano-rods (ZnO NRs) surface. XRD, Zeta potential, FESEM, EDS and XPS were hired for the characterization of ZnO-SiO2 nanohybrid system and applicability of GMZnO–Si mortar was investigated against microbial species (E. coli, S. aureus, A. niger). MIC/MBC/MFC values, agar plating, Inner permeability assay and ROS generation results exhibited excellent mechanistic approaches, by showing its ability to resist the biogenic degradation. The mechanical and durability activities of the GMZnO–Si are found considerably higher in respect to conventional control samples. The experimental outcomes propose a promising way to inclusion of ZnO-SiO2 modified geopolymer for biodeterioration-resistant structure with significant mechanical properties in near future.