Plant viruses have been widely used as templates for the synthesis of organic–inorganic hybrids. However, the fine-tuning of hybrid nanoparticle structures, especially the control of inorganic particle size as well as where the silication occurs (i.e. outside and/or inside of the capsid), by simply tuning the pH remains a challenge. By taking advantage of the templating effect of Cowpea Chlorotic Mottle Virus (CCMV) protein cages, we show that the silication at the exterior or interior surface of protein capsids, as well as the resulting structures of silica/virus hybrid nanoparticles can be fine-tuned by pH. At pH 4.0, only small silica particles (diameter of 2.5 nm) were formed inside the protein cages; at pH 6.0, silication mainly takes ...