Research interests in two-dimensional (2D) materials have seen exponential growth owing to their unique and fascinating properties. The highly exposed lattice planes coupled with tunable electronic states of 2D materials have created manifold opportunities in the design of new platforms for energy conversion and sensing applications. Still, challenges in understanding the electrochemical characteristics of these materials arise from the complexity of both intrinsic and extrinsic heterogeneities that can obscure structure–activity correlations. Scanning electrochemical probe microscopic investigations offer unique benefits in disclosing local electrochemical reactivities at the nanoscale level that are otherwise inaccessible with macroscale methods. This review summarizes recent progress in applying techniques of scanning electrochemical microscopy (SECM) and scanning electrochemical cell microscopy (SECCM) to obtain distinctive insights into the fundamentals of 2D electrodes. We showcase the capabilities of electrochemical microscopies in addressing the roles of defects, thickness, environments, strain, phase, stacking, and many other aspects in the heterogeneous electron transfer, ion transport, electrocatalysis, and photoelectrochemistry of representative 2D materials and their derivatives. Perspectives for the advantages, challenges, and future opportunities of scanning electrochemical probe microscopy investigation of 2D structures are discussed.