The influence of oxygen on the electrochemical response of magnesium–scandium (Mg–Sc) thin film electrodes has been investigated. It was found that the impact of oxygen dissolved in the electrolyte is two-fold. Firstly, it gives rise to a mixed-potential under open-circuit conditions that is much more positive than the true equilibrium potential of the hydride material, thus yielding incorrect thermodynamic data. Secondly, it causes self-oxidation of the hydrogenated thin films, making calculations regarding hydrogen storage capacities (mAh/g) not straightforward. A novel oxygen-scrubbing device was developed to de-oxygenate the argon used as purging gas during the electrochemical measurements. This self-regenerative system is based on the high reactivity of the methylviologen single radical towards oxygen. A comparison between various electrochemical responses of identical Mg–Sc thin film electrodes, measured with and without the presence of oxygen, showed distinct deviations in equilibrium potential and hydrogen storage capacity.