Although an isolated individual molecule clearly has only one ionization potential, multiple values are found for molecules in ordered assemblies. Photoelectron spectroscopy of archetypical pi-conjugated organic compounds on metal substrates combined with first-principles calculations and electrostatic modelling reveal the existence of a surface dipole built into molecular layers. Conceptually different from the surface dipole at metal surfaces, its origin lies in details of the molecular electronic structure and its magnitude depends on the orientation of molecules relative to the surface of an ordered assembly. Suitable pre-patterning of substrates to induce specific molecular orientations in subsequently grown films thus permits adjusting the ionization potential of one molecular species over up to 0.6 eV via control over monolayer morphology. In addition to providing in-depth understanding of this phenomenon, our study offers design guidelines for improved organic-organic heterojunctions, hole- or electron-blocking layers and reduced barriers for charge-carrier injection in organic electronic devices.