Inverted polymer solar cells based on P3HT/PCBM bulk heterojunction were prepared on flexible polyethylene naphthalate (PEN) substrate. The effect of annealing of the PEN/ITO/ZnO multilayer and ZnO/P3HT:PCBM on the structural, morphological, photophysical and photovoltaic properties was investigated and scrutinized directly on the OPV devices using atom probe tomography (APT), scanning electron microscopy (SEM) and microfocus X-ray techniques. We carried out a 3D reconstruction of the interfaces of the multilayer containing PEN/ITO, ZnO/ITO and P3HT:PCBM/ZnO to address the interface micro-structure and its influence on the morphology of the photoactive film. The analyses show that the morphology of the interfaces is affected by the structure of each layer of the BHJ devices causing orientation of P3HT crystals with PCBM aggregates and ZnO, which in turn leads to a significant change of the charge transport across each layer and therefore photovoltaic performances.