Quantum effects in plasmonic systems play an important role in defining the optical response of structures with subnanometer gaps. Electron tunneling across the gaps can occur, altering both the far-field optical response and the near-field confinement and enhancement. In this study, we experimentally and theoretically investigate plasmon coupling in gold "nanomatryoshka" (NM) nanoparticles with different core–shell separations. Plasmon coupling effects between the core and the shell become significant when their separation decreases to 15 nm. When their separation decreases to below 1 nm, the near- and far-field properties can no longer be described by classical approaches but require the inclusion of quantum mechanical effects such as electron transport through the self-assembled monolayer of molecular junction. In addition, surface-enhanced Raman scattering measurements indicate strong electron-transport induced charge transfer across the molecular junction. Our quantum modeling provides an estimate for the AC conductances of molecules in the junction. The insights acquired from this work pave the way for the development of novel quantum plasmonic devices and substrates for surface-enhanced Raman scattering.