Identification of nanoparticles in lysine−silica mixtures by SAXS analysis and cryo-TEM (see image) is reported. Initial stages of formation mimic that for tetrapropylammonium− and other alkylammonium−silica nanoparticles. The tunable porosity and morphology of thin films and gels synthesized from these sols have potential implications for novel biocompatible silicates and nanocomposites.