Energy storage and conversion systems are an integral component of emerging green technologies, including mobile electronic devices, automotive, and storage components of solar and wind energy economics. Despite the rapidly expanding manufacturing capabilities and wealth of phenomenological information on the macroscopic device behaviors, the microscopic mechanisms underpinning battery and fuel cell operations in the nanometer–micrometer range are virtually unknown. This lack of information is due to the dearth of experimental techniques capable of addressing elementary mechanisms involved in battery operation, including electronic and ion transport, vacancy injection, and interfacial reactions, on the nanometer scale. In this article, a brief overview of scanning probe microscopy (SPM) methods addressing nanoscale electrochemical functionalities is provided and compared with macroscopic electrochemical methods. Future applications of emergent SPM methods, including near field optical, electromechanical, microwave, and thermal probes and combined SPM-(S)TEM (scanning transmission electron microscopy) methods in energy storage and conversion materials are discussed.