Polyoxometalate cluster anions (POMs) control formation and morphology, and serve as protecting ligands, for structurally and compositionally diverse nanostructures. While numerous examples of POM-protected metal(0) nanoparticle syntheses and reactions can now be found in the literature, the use of POMs to prepare nano-scale analogs of binary inorganic materials, such as metal-oxides, sulfides and halides, is a relatively recent development. The first part of this critical review summarizes the use of POMs as protecting ligands for metal(0) nanoparticles, as well as their use as templates for the preparation of new inorganic materials. Here, key findings that reveal general trends are given additional emphasis. In the second part of the review, new information concerning the structure of POM-protected metal(0) nanoparticles is systematically developed. This information, obtained by the combined use of cryogenic transmission microscopy (cryo-TEM) and UV-vis spectroscopy, provides a new perspective on the formation and structure of POM-decorated nanoparticles, and on the rational design of catalytic and other functional POM-based nano-assemblies.