Targeted doping of grain boundaries is widely pursued as a pathway for combating thermal instabilities in nanocrystalline metals. However, certain dopants predicted to produce grain‐boundary‐segregated nanocrystalline configurations instead form small nanoprecipitates at elevated temperatures that act to kinetically inhibit grain growth. Here, thermodynamic modeling is implemented to select the Mo–Au system for exploring the interplay between thermodynamic and kinetic contributions to nanostructure stability. Using nanoscale multilayers and in situ transmission electron microscopy thermal aging, evolving segregation states and the corresponding phase transitions are mapped with temperature. The microstructure is shown to evolve through a transformation at lower homologous temperatures (<600 °C) where solute atoms cluster and segregate to the grain boundaries, consistent with predictions from thermodynamic models. An increase in temperature to 800 °C is accompanied by coarsening of the grain structure via grain boundary migration but with multiple pinning events uncovered between migrating segments of the grain boundary and local solute clustering. Direct comparison between the thermodynamic predictions and experimental observations of microstructure evolution thus demonstrates a transition from thermodynamically preferred to kinetically inhibited nanocrystalline stability and provides a general framework for decoupling contributions to complex stability transitions while simultaneously targeting a dominant thermal stability regime.

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