The energy level alignment in metal-organic and organic-organic junctions of the widely used materials tris-(8-hydroxyquinoline)aluminum (Alq3) and 1,4,5,8-naphthalenetetracarboxylic dianhydride (NTCDA) is investigated. The measured alignment schemes for single and bilayer films of Alq3 and NTCDA are interpreted with the integer charge transfer (ICT) model. Single layer films of Alq3 feature a constant vacuum level shift of ∼0.2–0.4 eV in the absence of charge transfer across the interface. This finding is attributed to the intrinsic dipole of the Alq3 molecule and (partial) ordering of the molecules at the interfaces. The vacuum level shift changes the onset of Fermi level pinning, as it changes the energy needed for equilibrium charge transfer across the interface.