Grain boundary segregation can reduce the driving force for grain growth in nanocrystalline materials and help retain fine grain sizes. However, grain boundary segregation is enthalpically driven, and so a stabilized nanocrystalline state should undergo a disordering process as temperature is increased. Here we develop a Monte Carlo-based simulation that determines the minimum free energy state of an alloy with a strong tendency for grain boundary segregation that considers both different grain sizes and a large solute configuration space. We find that a stable nanocrystalline alloy undergoes a disordering process where grain boundary segregated atoms dissolve into the adjacent grains and increase the grain size as a function of temperature. At a critical temperature, the single crystal state becomes the most preferred. Using this method, we are able to determine how the grain size changes as a function of temperature and produce equilibrium phase diagrams for nanocrystalline alloys.