Here, we report an in situ study of the effect of morphological/structural aging processes on polymer-based photovoltaic cell performances. The devices were provided with a fullerene film as a barrier layer between the active element and the metallic cathode. The experimental method adopted consists of the joint use of atomic force microscopy (AFM) and energy dispersive X-ray reflectivity (EDXR), an original coupling particularly effective in the study of stratified media. These techniques were applied first to the intermediate stages of the device construction and, finally, to a complete cell. The problems related with the surface/interface modifications of the devices elements in operating conditions were investigated in depth, with particular concern on the role of the C60 barrier layer. The C60 film surface topography was monitored by AFM experiments during illumination, which evidenced a surface reorganization of the C60 layer molecules over time. Conversely, the C60 film bulk and its interface with the active layer, investigated by EDXR analysis in the same conditions, turned out to remain unchanged. Then the cathode buried interface of a complete cell was studied, by EDXR measurements in working conditions, thus demonstrating that the C60 layer guarantees a good structural stability of the cell. In addition, the in situ AFM/EDXR characterization established that the observed reorganization process of the C60 layer molecules does not affect the film physical barrier role. This finding was confirmed by power conversion efficiency measurements, showing that the C60/LiF/Al cathode cell efficiency is preserved over time. This work also demonstrates how the morphological properties of organic device layered components, investigated in situ by the two noninvasive and independent AFM and EDXR techniques, may provide a structural interpretation of the performance preservation or fading.