The effect of natural electrode contamination on interfacial energetic, structure and morphology of π-conjugated organic molecular layers were studied by depositing dinapthothienothiophene (DNTT) thin films of varying thickness on indium-tin-oxide (ITO) substrates and by using photoelectron spectroscopy, atomic force microscopy and X-ray reflectivity techniques. The DNTT thin film on unclean-ITO surface shows a smaller threshold ionization potential (by ∼0.4 eV) compared to the film on clean-ITO one. A molecule–substrate interaction, present in the DNTT/clean-ITO system, gives rise to an interfacial dipole and charge transfer, presumably through flat-lying seed-layer at the interface. On further deposition, the interfacial coverage increases, while the molecules on top of the seed-layer take different orientation (mostly edge-on) to form highly-dewetted fibrous-islands of very high-thickness but very low-coverage. Overall, the growth of DNTT film on clean-ITO surface is layer-plus-island-like or Stranski–Krastanov-type. On the other hand, the contamination layer at the DNTT/unclean-ITO interface is found to act as a spacer layer, which reduces the intimate molecule–substrate interaction and also the roughness to give rise an edge-on ordered island-like or Volmer–Weber-type film-growth with reduced hole injection barrier (by ∼0.2 eV) and better (almost double) film-coverage to make it a more efficient hole injector compared to the clean interface one.