Organic nanowires and microfibers are excellent model systems for charge transport in organic semiconductors under nanoscopic confinement and may be relevant for future nanoelectronic devices. For this purpose, however, the preparation of well-ordered organic nanowires with uniform lateral dimensions remains a challenge to achieve. Here, we used the self-assembly of oligopeptide-substituted perylene bisimides and quaterthiophenes to obtain ‘well-ordered’ nanofibrils. The individual nanofibrils were investigated by spectroscopic and imaging methods, and the preparation of hierarchically structured microfibers of aligned nanofibrils allowed for a comprehensive structural characterization on all length scales with molecular level precision. Thus, we showed that the molecular chirality resulted in supramolecular helicity, which apparently serves to suppress lateral aggregation so that the individual nanofibrils comprised a single stack of the π-conjugated molecules at their core. Moreover, the conformational flexibility between the hydrogen-bonded oligopeptides and the π–π stacked chromophores gave rise to synergistically enhanced strong π–π interactions and hydrogen-bonding. The result is a remarkably tight π–π stacking inside the nanofibrils, irrespective of the electronic nature of the employed chromophores, which may render them suitable nanowire models to investigate one-dimensional charge transport along defined π-π stacks of p-type or n-type semiconductors.