The formation of hierarchical nanostructures using preformed dumbbell-like species made of covalent organic–inorganic polyoxometalate (POM)-based hybrid is herein described. In this system, the presence of charged subunits (POM, metal linker, and counter ions) in the complex molecular architecture can drive their aggregation, which results from a competition between the solvation energy of the discrete species and intermolecular electrostatic interactions. We show that the nature of the POM and the charge of the metal linker are key parameters for the hierarchical nanoorganization. The experimental findings were corroborated with a computational investigation combining DFT and molecular dynamic simulation methods, which outlines the importance of solvation of the counter ion and POM/counter ion association in the aggregation process. The dumbbell-like species can also form gels, in the presence of a poorer solvent, displaying similar nano-organization of the aggregates. We show that starting from designed molecular building units whose internal charges can be controlled by redox trigger we can achieve their implementation into soft nanostructured materials through the control of their supramolecular organization.