Polyoxometalates (POMs) are redox-active molecular oxides, which attract growing interest for their integration into nano-devices, such as high-density data storage non-volatile memories. In this work, we investigated the electrostatic deposition of the negatively charged [H7P8W48O184]33− POM onto positively charged 8-amino-1-octanethiol self-assembled monolayers (SAMs) preformed onto gold substrates or onto an array of gold nanodots. The ring-shaped [H7P8W48O184]33− POM was selected as an example of large POMs with high charge storage capacity. To avoid the formation of POM aggregates onto the substrates, which would introduce variability in the local electrical properties, special attention has to be paid to the preformed SAM seeding layer, which should itself be deprived of aggregates. Where necessary, rinsing steps were found to be crucial to eliminate these aggregates and to provide uniformly covered substrates for subsequent POM deposition and electrical characterizations. This especially holds for commercially available gold/glass substrates while these rinsing steps were not essential in the case of template stripped gold of very low roughness. Charge transport through the related molecular junctions and nanodot molecule junctions (NMJs) has been probed by conducting-AFM. We analyzed the current–voltage curves with different models: electron tunneling though the SAMs (Simmons model), transition voltage spectroscopy (TVS) method or molecular single energy level mediated transport (Landauer equation) and we discussed the energetics of the molecular junctions. We concluded to an energy level alignment of the alkyl spacer and POM lowest occupied molecular orbitals (LUMOs), probably due to dipolar effects.