Intercalated metal nanoclusters (NCs) can be formed under the surface of graphite after sputtering to generate surface “portal” defects that allow deposited atoms to reach the subsurface gallery. However, there is a competition between formation of supported NCs on top of the surface and intercalated NCs under the surface, the latter only dominating at sufficiently high temperature. A stochastic model incorporating appropriate system thermodynamics and kinetics is developed to capture this complex and competitive nucleation and growth process. Kinetic Monte Carlo simulation shows that the model captures experimental trends observed for Cu and other metals and reveals that higher temperatures are needed to facilitate detachment of atoms from supported NCs enabling them to reach the gallery.