By coupling a cluster expansion with density functional theory (DFT) calculations, we determine the configurational thermodynamics (site preferences and occupations) for alloyed nanoparticles (NPs) as functions of composition (c) and temperature (T), exemplified using a 55-atom Ag-Au truncated cuboctahedron NP. The c−T phase diagram for site occupations gives detailed design information for alloyed NP, especially the thermodynamically stable active sites for catalysis and how they change with stoichiometry and processing temperature. Generally, Ag prefers core and Au prefers shell, agreeing with our universal core-shell preference assessed from DFT impurity segregation energies but with interesting multishell configurations having specific active sites.