The organic surfactants like CTAB have long been used in numerous methods of chemical synthesis of nanoparticles effectively, in order to avoid agglomeration and provide stability. However, these are not really stable at higher temperatures. Hence, in this work, gold nanoparticles have been encapsulated with SiO2 shells along with CTAB surfactant molecules. The thermal behaviour and the associated physicochemical changes in the Au@SiO2 core-shell structures, during the Thermo Gravimetric Analysis (TGA), have been studied using several standard characterization techniques like Fourier Transform Infrared Spectroscopy, Transmission Electron Microscopy, X-ray Diffractometry and UV–Vis Absorption spectroscopy. About 40% weight loss has been observed during the TGA treatment. The TEM results show different stages of agglomeration after TGA, which includes expansion of SiO2 shells, out-diffusion of gold particles and their eventual agglomeration. Detailed FTIR analysis confirms the proposed mechanism, and is well complemented by TEM, XRD and UV–Vis Absorption results. Display omitted •Effect of thermal treatment and associated physicochemical changes of Au@SiO2 is studied.•The multi-step weight loss observed during thermal treatment.•Decomposition of CTAB molecules seems to have played major role in overall weight loss observed.•Softening of SiO2 shell, out-diffusion of gold particle has been presented.