A rigid bolaamphiphile molecule (NDI-1) was synthesized consisting of a naphthalenediimide unit with glutamic acid head groups. Co-assembly of NDI-1 with cyclam, spermine and melamine bearing amine functional groups is studied herein giving significantly different microstructures. NDI-1 was designed to induce geometrically favourable hydrogen bonding with its counterpart molecules in the co-assembly to trigger supramolecular micro- and nano-architectures formation. The interaction between the bolaamphiphile NDI-1 and biologically important amines such as cyclam, spermine and melamine was investigated by UV-vis and fluorescence emission spectroscopy and the nanostructure morphology was studied using scanning electron microscopy. It was found that the co-assembly of NDI-1 with cyclam resulted in fractal-like morphology. Co-assembly of NDI-1 with spermine yielded a crystalline microstructure based on an alpha-helix molecular arrangement changed into a quasicrystal structure. Self-assembly of NDI-1 in the presence of melamine resulted in a highly crystalline needle-like morphology. The nucleation and growth of the nanostructures were tuned by analytes into distinct classes. Such changes in morphology are significant to the fabrication of various nanomaterials via non-covalent interactions with distinct properties.