Ab initio electronic structure calculations, within the Kohn–Sham scheme of the density functional theory, are often considered reliable and a powerful tool to provide ground state information on intermetallic compounds. More recently, it has been used in multi-scale intermetallic phase diagram calculations with particular importance when experimental data is lacking. In spite of this recent success, they rely on basic choices of the computational solution of the complicated quantum mechanical problem. Therefore, the calculated phase diagrams may depend on these choices. Here, we concentrate on the influence of some methodological aspects of the ab initio calculations on the resulting phase diagram, for a given statistical mechanics approach. We use the Full Potential-Linear Augmented Plane Wave and the Projector Augmented Wave Methods to perform electronic structure calculations combined with the cluster variation method in the irregular tetrahedron approximation to calculate the BCC Mo–Fe phase diagram. It is shown that all calculated phase diagrams present similar qualitative features (an asymmetric miscibility gap), but quantitative variations are found depending on some of the basic assumptions adopted for the electronic structure calculations. Based on these results, a “natural” accuracy of the order of ± 1 kJ mol−1 can be estimated for ab initio compound formation energies.