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Abstract Transparent microelectrodes have received much attention from the biomedical community due to their unique advantages in concurrent crosstalk‐free electrical and optical interrogation of cell/tissue activity. Despite recent progress in constructing transparent microelectrodes, a major challenge is to simultaneously achieve desirable mechanical stretchability, optical transparency, electrochemical performance, and chemical stability for high‐fidelity, conformal, and stable interfacing with soft tissue/organ systems. To address this challenge, we have designed microelectrode arrays (MEAs) with gold‐coated silver nanowires (Au–Ag NWs) by combining technical advances in materials, fabrication, and mechanics. The Au coating improves both the chemical stability and electrochemical impedance of the Au–Ag NW microelectrodes with only slight changes in optical properties. The MEAs exhibit a high optical transparency >80% at 550 nm, a low normalized 1 kHz electrochemical impedance of 1.2–7.5 Ω cm², stable chemical and electromechanical performance after exposure to oxygen plasma for 5 min, and cyclic stretching for 600 cycles at 20% strain, superior to other transparent microelectrode alternatives. The MEAs easily conform to curvilinear heart surfaces for colocalized electrophysiological and optical mapping of cardiac function. This work demonstrates that stretchable transparent metal nanowire MEAs are promising candidates for diverse biomedical science and engineering applications, particularly under mechanically dynamic conditions.