Understanding chemical degradation at the interface between different layers in an organic photovoltaic device (OPV) is crucial to improving the long‐term stability of OPVs. Herein, molecular‐level insights are provided into the impact of different metal top electrodes on the interfacial morphology and stability of photoactive layers in PM6:Y6 bulk‐heterojunction (BHJ) OPVs. OPVs with an aluminum (Al) top electrode exhibit inferior stability compared to silver (Ag) electrode devices upon thermal annealing, whereby thermal stress induces the diffusion of both Al and Ag atoms to the PM6:Y6 BHJ layer. The diffused Al atoms cause surface recombination at the interface between the photoactive layer and an interlayer. Specifically, X‐ray photoelectron spectroscopy suggests the different local chemical environments of PM6 and Y6 moieties in PM6:Y6/Al‐contact devices. These results are corroborated by solid‐state nuclear magnetic resonance and electron paramagnetic resonance spectroscopy measurements, indicating the formation of ionic and organo‐metallic‐like species at the sub‐layers of the PM6:Y6 BHJ morphology, which are estimated to be less than 5 wt% of the PM6:Y6/Al blend. By comparison, the Ag atoms do not adversely affect PM6:Y6 BHJ morphology and the associated device physics. The investigation of reactive electrode‐BHJ interfaces by multiscale characterization techniques and device physics is expected to provide guidance to future interfacial engineering strategies to develop stable and efficient OPVs.