Plasmonic superstructures (PS) based on Au/SiO2 were prepared for Shell-Isolated Nanoparticle-Enhanced Raman Spectrocopy (SHINERS) in liquid phase applications. These superstructures are composed of functionalized SiO2 spheres with plasmonic Au nanoparticles (NPs) on their surface. Functionalization was performed with (3-aminopropyl)trimethoxysilane, (3-mercaptopropyl)trimethoxysilane and poly(ethylene-imine) (PEI). Of these three, PEI-functionalized spheres showed the highest adsorption density of Au NPs in TEM, UV-Vis and DLS experiments. Upon decreasing the Au NP/SiO2 sphere size ratio, an increase in adsorption density was also observed. To optimize plasmonic activity, 61 nm Au NPs were adsorbed onto 900 nm SiO2-PEI spheres and these PS were coated with an ultrathin layer (1-2 nm) of SiO2 to obtain Shell-Isolated Plasmonic Superstructures (SHIPS), preventing direct contact between Au NPs and the liquid medium. Zeta potential measurements, TEM and SHINERS showed that SiO2 coating was successful. The detection limit for SHINERS using SHIPS and a 638 nm laser was around 10-12 M of Rhodamine (10-15 M for uncoated PS), all with acquisition settings suitable for catalysis applications.