By promoting tissue regeneration, porous nano‐scaffolds offer improved chances for the maintenance, repair, and enhancement of damaged tissues and organ functioning. In this study, the nanosilica extract obtained from the agricultural waste, that is, rice husk after surface modification shows higher hydrophobicity in the hexamethyldisilazane and methyltrimethoxysilane‐modified nanosilica and hydrophilic nature in 3‐aminopropyl triethoxysilane‐modified nanosilica. Fourier transform infrared spectroscopy results reveal the functional groups exist in the scaffold and its surface morphology was evaluated by Field emission scanning electron microscope/energy dispersive X‐ray analysis which shows a cross‐network structure that could impart the proper cell adhesion. The presence of amorphous nanosilica in ultrapure form was confirmed using X‐ray diffraction analysis where a broad peak was obtained in the range of 15°–40°. The crystallization phase of the hybrid scaffold shows 2θ values obtained at 22.6°, 28.7°, and 40.6°. The graph thus obtained confirms that the material used is 3‐aminopropyl‐triethoxysilane‐modified silk/silica nanocomposite. The decomposition rates and temperature of the composite were analyzed using the thermogravimetry/differential thermal technique. The antibacterial activity of the hybrid scaffolds and silk and silica shows the metabolic pathways were not disrupted for both Gram‐positive and ‐negative microbes. Cell cytotoxicity analysis proved that the electrospun hybrid scaffold was nontoxic to L929 cells and promoted cell adhesion and growth. The cells were highly proliferated onto the surface layers in a regular systematic pattern thus proving that these scaffolds were suitable for bone regeneration applications. Hence these economically viable scaffolds turn to be biocompatible and are promising as a novel product for cell culture regneration realted to therapy.