In the present work, an insight on the morpho/structural properties of semitransparent organic devices for buildings’ integrated photovoltaics is presented, and issues related to interface and bulk stability are addressed. The organic photovoltaic (OPV) cells under investigation are characterized by a blend of PM6:Y6 as a photo-active layer, a ZnO ETL (electron transporting layer), a HTL (hole transporting layer) of HTL-X and a transparent electrode composed by Ag nanowires (AgNWs). The devices’ active nanomaterials, processed as thin films, and their mutual nanoscale interfaces are investigated by a combination of in situ Energy Dispersive X-ray Reflectometry (EDXR) and ex situ Atomic Force Microscopy (AFM), X-ray Diffraction (XRD) and micro-Raman spectroscopy. In order to discriminate among diverse concomitant aging pathways potentially occurring upon working conditions, the effects of different stress factors were investigated: light and temperature. Evidence is gained of an essential structural stability, although an increased roughness at the ZnO/PM6:Y6 interface is deduced by EDXR measurements. On the contrary, an overall stability of the system subjected to thermal stress in the dark was observed, which is a clear indication of the photo-induced origin of the observed degradation phenomenon. Micro-Raman spectroscopy brings light on the origin of such effect, evidencing a photo-oxidation process of the active material in the device, using hygroscopic organic HTL, during continuous illumination in ambient moisture conditions. The process may be also triggered by a photocatalytic role of the ZnO layer. Therefore, an alternative configuration is proposed, where the hygroscopic HTL-X is replaced by the inorganic compound MoOx. The results show that such alternative configuration is stable under light stress (solar simulator), suggesting that the use of Molybdenum Oxide, limiting the photo-oxidation of the bulk PM6:Y6 active material, can prevent the cell from degradation.