Nowadays, the development of devices based on organic materials is an interesting research challenge. The performance of such devices is strongly influenced by material selection, material properties, design, and the manufacturing process. Usually, buckminsterfullerene (C60) is employed as electron transport material in organic photovoltaic (OPV) devices due to its high mobility. However, considering its low solubility, there have been many attempts to replace it with more soluble non-fullerene compounds. In this study, bulk heterojunction thin films with various compositions of zinc phthalocyanine (ZnPc), a perylene diimide derivative, or C60 were prepared by matrix-assisted pulsed laser evaporation (MAPLE) technique to assess the influence of C60 replacement on fabricated heterostructure properties. The investigations revealed that the optical features and the electrical parameters of the organic heterostructures based on this perylene diimide derivative used as an organic acceptor were improved. An increase in the JSC value (4.3 × 10−4 A/cm2) was obtained for the structures where the perylene diimide derivative acceptor entirely replaced C60 compared to the JSC value (7.5 × 10−8 A/cm2) for the heterostructure fabricated only with fullerene. These results are encouraging, demonstrating the potential of non-fullerene compounds as electron transport material in OPV devices.