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We present an ab-initio-based effective interaction model (EIM) for the study of magnetism, thermodynamics, and their interplay in body-centered cubic Fe-Co alloys, with Co content from 0 to 70%. The model includes explicitly both spin and chemical variables. For the former, a Heisenberg formalism is adopted. But, the spin magnitude of each Fe atom varies according to its local chemical environment, following a simple rule determined by density functional theory (DFT) calculations. The proposed model is able to describe precisely the ground-state magneto-energetic landscape of both chemically ordered and disordered Fe-Co systems, as given by DFT and experiments. In combination with on-lattice Monte Carlo simulations, it enables an accurate prediction at finite temperatures. In particular, the Curie point and the chemical order-disorder (B2-A2) transition temperature are accurately predicted, for all the concentrations considered. A strong dependency of the chemical transition temperature on the magnetic configuration is evidenced and analyzed. We also suggest a more important effect of magnetic rather than vibrational entropy on the chemical transition. However, this transition is not affected by a commonly accessible external magnetic field.