The growth of atomically dispersed metal catalysts (ADMCs) remains a great challenge owing to the thermodynamically driven atom aggregation. Here we report a surface-limited electrodeposition technique that uses site-specific substrates for the rapid and room-temperature synthesis of ADMCs. We obtained ADMCs by the underpotential deposition (UPD) of a single-atom nonnoble metal onto the chalcogen atoms of chemically exfoliated transition metal dichalcogenides and subsequent galvanic displacement with a more-noble single-atom metal. The site-specific electrodeposition (SSED) enables the formation of energetically favorable metal–support bonds, and then automatically terminates the sequential formation of metallic bonding. The self-terminating effect restricts the metal deposition to the atomic scale. The modulated ADMCs exhibit remarkable activity and stability in the hydrogen evolution reaction compared to state-of-the-art single-atom electrocatalysts. We demonstrate that this SSED methodology could be extended to the synthesis of a variety of ADMCs (for example, Pt, Pd, Rh, Cu, Pb, Bi, and Sn single atoms), showing its general scope for the large-scale production of functional ADMCs in heterogenous catalysis.