We study the thermodynamics of C incorporation on Si(100), a system where strain and chemical effects are both important. Our analysis is based on first-principles atomistic calculations to obtain the important lowest-energy structures, and a classical effective Hamiltonian which is employed to represent the long-range strain effects and incorporate the thermodynamic aspects. We determine the equilibrium phase diagram in temperature and C chemical potential, which allows us to predict the mesoscopic structure of the system that should be observed under experimentally relevant conditions.