The chemical and physical properties of molecules and materials are known to be modified significantly under vibrational strong coupling (VSC). To gain insight into the effects of VSC on π–π interactions involved in molecular self-assembly, themselves sensitive to vacuum electromagnetic field fluctuations, the aggregation of two structural isomers (linear and V-shaped) of phenyleneethynylene under cooperative coupling was investigated. By coupling the aromatic C═C stretching band, the assembly of one of the molecules results in the formation of spheres as opposed to flakes under normal conditions. As a consequence, the electronic absorption and emission spectra of the self-assembled structures are also modified significantly. The VSC-induced changes depend not only on the type of vibration that is coupled but also on the symmetry of the phenyleneethynylene isomer. These results confirm that VSC can be used to drive molecular assemblies to new structural minima and thereby provide a new tool for supramolecular chemistry