Shell-isolated gold nanoparticles (SHINs) were employed to record shell-isolated nanoparticle-enhanced Raman spectra (SHINERS) of a passive layer formed at a gold surface during gold leaching from thiosulfate solutions. The (3-aminopropyl)triethoxysilane (APTES) and a sodium silicate solution were used to coat gold nanoparticles with a protective silica layer. This protective silica layer prevented interactions between the thiosulfate electrolyte and the gold core of the SHINs when the SHINs-modified gold electrode was immersed into the thiosulfate lixiviant. The SHINERS spectra of the passive layer, formed from thiosulfate decomposition, contained bands indicative of hydrolyzed APTES. We have demonstrated how to exploit the presence of these APTES bands as an internal standard to compensate for fluctuations of the surface enhancement of the electric field of the photon. We have also developed a procedure that allows for removal of the interfering APTES bands from the SHINERS spectra. These methodological advancements have enabled us to identify the species forming the passive layer and to determine that the formation of elemental sulfur, cyclo-S8, and polymeric sulfur chains is responsible for inhibition of gold dissolution in oxygen rich thiosulfate solutions.