Organic bilayer solar cells based on a donor/acceptor junction of zinc-phthalocyanine/1,4-diaminoanthraquinone (ZnPc/1,4-DAAQ) were studied. The transparent conductive oxide (TCO) electrode used was either the indium tin oxide (ITO) or the zinc oxide (ZnO), also the (poly(3,4-ethylenedioxythiophene):poly(styrene sulfonic acid (PEDOT:PSS) was used as conductive polymer. Two different configurations were prepared: glass/ITO (or ZnO)/ZnPc/1,4-DAAQ/Al configuration and glass/Al/1,4-DAAQ/ZnPc/PEDOT:PSS/ ITO (or ZnO)/glass configuration. From the analysis of the current–voltage characteristics, the former presented a fill factor of 0.2, whereas the latter showed a fill factor of 0.5. Scanning electron microscopy images of the surface of the 1,4-DAAQ layer and the cross section of the overall structure were obtained. 1,4-DAAQ films revealed a highly fibrillar morphology. This special morphology is thought to have a preponderant effect on the fill factor, depending on the cell configuration.