The energy‐level alignment (ELA) at interfaces ubiquitous in organic optoelectronic applications is decisive for the device performance. Due to the notoriously low density of free charge carriers in organic thin films, the ELA at organic––inorganic interfaces is determined by gap states and/or tailing states of the frontier molecular orbitals, that is, the highest occupied molecular orbital and the lowest unoccupied molecular orbital (LUMO). Informed by modeling defect energies on the density‐functional theory level, it is deduced from ultraviolet and X‐ray photoelectron spectroscopy data that chemical‐defect induced gap states lead to the substrate‐independent pinning of the Fermi level (EF) to the LUMO for 1,4,5,8,9,12‐hexaazatriphenylene‐2,3,6,7,10,11‐hexacarbonitrile thin films. For 5,6,11,12,17,18‐hexaazatrinaphthylene thin films, the ELA is instead governed by tailing states due to energetic disorder, which put the EF closer to midgap position. It is highlighted in the study that the susceptibility of conjugated organic material to forming chemical and structural defects is key for the ELA at interfaces and, therefore, must be considered in the synthesis of novel materials and their processing into functional structures.