Surface-enhanced Raman scattering (SERS) is a powerful spectroscopy technique that can provide non-destructive and ultra-sensitive characterization down to single molecular level, comparable to single-molecule fluorescence spectroscopy. However, generally substrates based on metals such as Ag, Au and Cu, either with roughened surfaces or in the form of nanoparticles, are required to realise a substantial SERS effect, and this has severely limited the breadth of practical applications of SERS. A number of approaches have extended the technique to non-traditional substrates, most notably tip-enhanced Raman spectroscopy (TERS) where the probed substance (molecule or material surface) can be on a generic substrate and where a nanoscale gold tip above the substrate acts as the Raman signal amplifier. The drawback is that the total Raman scattering signal from the tip area is rather weak, thus limiting TERS studies to molecules with large Raman cross-sections. Here, we report an approach, which we name shell-isolated nanoparticle-enhanced Raman spectroscopy, in which the Raman signal amplification is provided by gold nanoparticles with an ultrathin silica or alumina shell. A monolayer of such nanoparticles is spread as 'smart dust' over the surface that is to be probed. The ultrathin coating keeps the nanoparticles from agglomerating, separates them from direct contact with the probed material and allows the nanoparticles to conform to different contours of substrates. High-quality Raman spectra were obtained on various molecules adsorbed at Pt and Au single-crystal surfaces and from Si surfaces with hydrogen monolayers. These measurements and our studies on yeast cells and citrus fruits with pesticide residues illustrate that our method significantly expands the flexibility of SERS for useful applications in the materials and life sciences, as well as for the inspection of food safety, drugs, explosives and environment pollutants.