The preferential oxidation of CO (CO-PrOx) to CO2 is an effective catalytic process for purifying the H2 utilized in proton-exchange membrane fuel cells for power generation. Our current work reports on the synthesis, characterization and CO-PrOx performance evaluation of unsubstituted and magnesium-substituted iron- and cobalt-based oxide catalysts (i.e., Fe3O4, Co3O4, MgFe2O4 and MgCo2O4). More specifically, the ability of Mg to stabilize the MgFe2O4 and MgCo2O4 structures, as well as suppress CH4 formation during CO-PrOx was of great importance in this study. The cobalt-based oxide catalysts achieved higher CO2 yields than the iron-based oxide catalysts below 225 °C. The highest CO2 yield (100%) was achieved over Co3O4 between 150 and 175 °C, however, undesired CH4 formation was only observed over this catalyst due to the formation of bulk fcc and hcp Co0 between 200 and 250 °C. The presence of Mg in MgCo2O4 suppressed CH4 formation, with the catalyst only reducing to a CoO-type phase (possibly containing Mg). The iron-based oxide catalysts did not undergo bulk reduction and did not produce CH4 under reaction conditions. In conclusion, our study has demonstrated the beneficial effect of Mg in stabilizing the active iron- and cobalt-based oxide structures, and in suppressing CH4 formation during CO-PrOx.