Silica-based nanostructures are among the most utilized materials. However, a persistent challenge is their irreversible agglomeration upon drying and heat treatments, restricting their homogeneous colloidal re-dispersion - a mandatory requirement for diverse bio-applications. We address this bottleneck by developing a self carbo-passivation (SCP) strategy: silica nanoparticles (NPs), pre-included with the catalytic metal precursors and organosilanes undergo in vacuo thermochemical conversion with highly controlled interior-to-surface segregation of nanometer-scale "carbonaceous skin patches". This self-generated inert passivate shielding phenomenon at the individual NP level completely inhibits interparticle cross-linking, stopping chemical agglomeration and enhancing colloidal stability. By SCP, we synthesized silica-based magnetic-catalytic nanoreactors for magnetic field-induced catalysis inside living cells, by benefitting from the convenient high colloidal stability in bio-media, easy endocytosis and protective accessibility to the catalytic site in the complex bio-environment. The present work demonstrates deep mechanistic insight into unexplored solid-state nanoscopic chemical passivation phenomena, dramatically influencing NP surface characteristics, playing a critical role in solution-based applications.