The energy level alignment at the pentacene/Au(111) and pentacene/SnS2 interfaces was determined using in situ thin film deposition in combination with X-ray and ultraviolet photoemission spectroscopy (UPS). The organic thin films were grown by vapor deposition in multiple steps and then sequentially characterized in situ after each growth step. The pentacene/Au(111) interface is an ohmic contact that yielded a strong (0.95 eV) interfacial dipole barrier. The vacuum-cleaved SnS2 single crystal substrates provided clean, atomically flat and chemically inert surfaces, allowing for the investigation of the core level energy shifts and interface dipoles without interference from chemical reactions or effects of the substrate morphology. Low-intensity X-ray photoemission work function measurements enabled the detection of the overlayer thickness-dependent onset of charging in the UPS measurements. This allowed for precise determination of the position of the highest occupied molecular orbital of the organic molecules at the investigated interfaces. Differences in the orientation of the pentacene molecules on the two substrates were proposed based on analysis of the UP spectra, scanning tunneling microscopy results of their films, and atomic force microscopy images of thick pentacene layers.