Ultraviolet photoelectron spectroscopy is used to investigate the energy level alignment and molecular orientation at the interfaces in Au/pentacene/PTCDA trilayer stacks. We deduced a standing orientation for pentacene grown on Au while we conclude a flat lying geometry for PTCDA grown onto pentacene. We propose that the rough surface of polycrystalline Au induces the standing geometry in pentacene. It is further shown that in situ deposition of PTCDA on pentacene can influence the orientation of the surface pentacene layer, flipping part of the surface pentacene molecules into a flat lying geometry, maximizing the orbital interaction across the pentacene-PTCDA heterojunction. Crown Copyright (C) 2013 Published by Elsevier B. V. All rights reserved.