Polyoxomolybdate-based organic−inorganic hybrid architectures were synthesised and characterised by X-ray crystallography. The supramolecular assemblies present rows of metallic clusters H-bonded by ammonium cations, with a 1:2 molybdate/ammonium ratio. The organic moieties of the ammonium cations establish hydrophobic contact among them such as van der Waals, C–H⋯π and π⋯π interactions that stabilise the supramolecular architectures. In particular, for compound 5 the n-alkyl tails pack closely together giving a lipid-like bilayer. In compound 6, the aromatic phenyl rings of the organic cation allow the stabilisation of the supramolecular architecture by C–H⋯π and π⋯π interactions. Regarding the X-ray structure of the compound 11, the tetraanionic octa-molybdate [Mo8O26]4− cluster is surrounded by four ethyl-triphenyl-phosphonium cations. Running along the b-axis open channels are occupied by DMF solvent molecules. Interestingly, a soaking experiment in n-pentane with the corresponding crystals of compound 11 afforded to a crystal structure very different from the native one. Van der Waals, C–H⋯π and π⋯π interactions between large organic moieties are fundamental in the stabilization of hybrid organic-inorganic POM architectures.