A silver–silica nano composite based geopolymer mortar has been developed by simple adsorption of silver in a suitable amount of a colloidal silica suspension for anti-bacterial property development. The silver nanoparticles (3–7 nm) were attached on the surface of 20–50 nm sized silica nanoparticles. The silver–silica nano-composite was characterized by Transmission Electron Microscopy (TEM), X-Ray Diffraction (XRD) and energy dispersive X-ray spectral analysis. Mechanical strength, durability and mechanistic anti-bacterial activity of the silver–silica nano composite modified geopolymer mortar (GM_Ag–Si) were investigated and compared to nano silica modified geopolymer mortar (GM_Si) and control cement mortar (CM). To accesses the anti-microbial efficacy of the samples, 99% mortality for Gram positive and Gram negative bacteria was calculated. Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC) values were determined from batch cultures. The addition of 6% (w/w) of the silver–silica nano composite in the geopolymer mortar cured at ambient temperature shows substantial improvement in mechanical strength, durability and anti-bacterial property. Reactive Oxygen Species (ROS) generation and cell wall rupture as observed from fluorescence microscopy and Field Emission Scanning Electron Microscopy (FESEM) may be possible reasons behind the anti-bacterial efficacy of silver–silica nano composite modified geopolymer mortar.