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Structurally regular nanopore arrays fabricated to contain independently controllable annular electrodes represent a new kind of architecture capable of electrochemically addressing small collections of matter—down to the single entity (molecule, particle, and biological cell) level. Furthermore, these nanopore electrode arrays (NEAs) can also be interrogated optically to achieve single entity spectroelectrochemistry. Larger entities such as nanoparticles and single bacterial cells are investigated by dark-field scattering and potential-controlled single-cell luminescence experiments, respectively, while NEA-confined molecules are probed by single molecule luminescence. By carrying out these experiments in arrays of identically constructed nanopores, massively parallel collections of single entities can be investigated simultaneously. The multilayer metal–insulator design of the NEAs enables highly efficient redox cycling experiments with large increases in analytical sensitivity for chemical sensing applications. NEAs may also be augmented with an additional orthogonally designed nanopore layer, such as a structured block copolymer, to achieve hierarchically organized multilayer structures with multiple stimulus-responsive transport control mechanisms. Finally, NEAs constructed with a transparent bottom layer permit optical access to the interior of the nanopore, which can result in the cutoff of far-field mode propagation, effectively trapping radiation in an ultrasmall volume inside the nanopore. The bottom metal layer may be used as both a working electrode and an optical cladding layer, thus, producing bifunctional electrochemical zero-mode waveguide architectures capable of carrying out spectroelectrochemical investigations down to the single molecule level.