Silica nanoparticles were synthesized through a versatile sol–gel combustion method from hydrazide based hypercoordinated silicon complexes derived from the reaction of silicon tetrachloride with O-silylated hydrazide derivatives. The complexes were characterized by ¹H, ¹³C, ²⁹Si NMR and ESI-mass spectrometric techniques. A refined morphology was observed in the product after sintering i.e. from spherical to rod shaped nanoparticles. The powder X-ray diffraction patterns and the TEM images of silica show the formation of silica nanoparticles. The IR spectra show Si–O linkages and DLS studies indicate the particle size distribution to be between 20 and 100 nm for the material before sintering and 70–120 nm after sintering at 1000 °C. A TEM image of the decomposed gel indicates the formation of crystalline silica rods. This work also demonstrates the influence of nano-sized silica particles on antibacterial activity (DIZ, MIC and MBC) i.e. better activity was shown for nano-rods derived from the hypercoordinated silicon complexes than the conventional TEOS (sol–gel) method. Experiments on the generation of reactive oxygen species (ROS) through oxidative stress demonstrate the toxicity of nanosilica particles.