In this study the performance differences of layered and bulk-heterojunction based organic solar cells composed of the prototypical p-and n-type organic semiconductors pentacene ͑PEN͒ and fullerene ͑C60͒ are correlated with the physical properties of the heterostructures. The electronic structure of layered and codeposited thin PEN and C60 films on the conducting polymer substrate poly͑ethylenedioxythiophene͒:poly͑styrenesulfonate͒ ͑PEDOT:PSS͒ was investigated with ultraviolet photoelectron spectroscopy. Layered structures of C60 on PEN precovered PEDOT:PSS exhibited an offset of the highest occupied molecular orbital ͑HOMO͒ levels of 1.45 eV. In contrast, codeposited films of PEN and C60 showed a reduced HOMO-level offset of 0.85 eV, which increased to 1.45 eV by precoverage of the substrate with a thin PEN layer. In this case, the PEN-HOMO level was Fermi-level pinned at 0.35 eV binding energy and charge transfer between PEN and PEDOT:PSS decreased the vacuum level by 0.75 eV. In addition, the morphology and crystal structure of the respective systems have been investigated by atomic force microscopy ͑AFM͒, x-ray diffraction ͑XRD͒ and Fourier-transform infrared spectroscopy, which indicated pronounced phase separation of PEN and C60 in the codeposited films. XRD revealed crystalline growth of PEN in all investigated cases forming crystallites that exceeded the nominal film thickness by an order of magnitude, whereas C60 was crystalline only if grown on the PEN precovered substrates. AFM investigations allowed to correlate morphology and structure revealing micro-and nanophase separation between PEN and C60.