Hollow siloxane-based nanoparticles (HSNs) have attracted significant attention because of their unique properties and applications. Recently, it was discovered that the simple covering of silica nanoparticles with an organosiloxane shell leads to the spontaneous formation of HSNs; however, the detailed mechanism of their formation has not yet been established. In this study, colloidal 30 nm HSNs were prepared by adding organically bridged alkoxysilane to an aqueous dispersion of mesostructured silica–surfactant composite nanoparticles, and the temporal changes of the morphology and chemical state of the nanoparticles were monitored to elucidate the formation mechanism. Core silica was dissolved after the formation of the core–shell structured nanoparticles, and almost all the dissolved silicate species were incorporated in the organosiloxane shell, changing the shell thickness. Two conditions were essential for silica dissolution induced by covering with organosiloxane: (i) presence of a sufficient amount of uncondensed Si–OH groups in the organosiloxane shell, and (ii) elevated temperature and pH for the promotion of the hydrolysis of silica. These findings will enable the fabrication of various HSNs through organosiloxane-induced silica dissolution and redeposition.