The effect of the partial substitution of S by Se atoms in the Mo6Se8−n S n Chevrel phases (CPs), (n =0, 1, 2), on the reversible intercalation of Mg ions into these hosts was studied by a combination of cyclic voltammetry (CV), galvanostatic cycling, potentiostatic intermittent titration (PITT) and electrochemical impedance spectroscopy (EIS) techniques. Based on the previously published structural characterizations of the CP compounds under study, we describe herein the thermodynamic effect of the substitution in terms of the transformation of a single peak of the differential capacitance for the pure Mo6X8 phases (X=S or Se), into a set of a lower amplitude and broader peaks for the mixed (S, Se) CPs, located at less positive potentials compared to that for the pure CP. This is due to the preferential ordering of the Se anions (as compared to that of S anions) in their sites in the CP's crystal structure. In addition to the thermodynamic effect of the substitution, the geometry of the transition state for the mobile Mg ions is modified, thus facilitating the insertion of Mg ions into the partially substituted CP compounds (the kinetic effect). Thereby, the partial charge trapping that characterizes Mg ion insertion into sulfide-based CPs at low temperatures vanishes in the Mg x Mo6S6Se2 compounds. This was nicely confirmed by impedance (EIS) measurements in combination with chronopotentiometry.