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Abstract Nanoscale manipulation and characterization of individual molecules is necessary to understand the intricacies of molecular structure, which governs phenomena such as reaction mechanisms, catalysis, local effective temperatures, surface interactions, and charge transport. Here we utilize Raman enhancement between two nanostructured electrodes in combination with direct charge transport measurements to allow for simultaneous characterization of the electrical, optical, and mechanical properties of a single molecule. This multi‐dimensional information yields repeatable, self‐consistent, verification of single‐molecule resolution, and allows for detailed analysis of structural and configurational changes of the molecule in situ. These experimental results are supported by a machine‐learning based statistical analysis of the spectral information and calculations to provide insight into the correlation between structural changes in a single‐molecule and its charge‐transport properties.