The field of tunnelling spintronics has flourished through the study of magnetic tunnel junctions (MTJs) with MgO barriers. The combination of high spintronic performance and low effective barrier heights has enabled new technologies, ranging from next-generation memories to bio-inspired computing. This combination is made possible by structural defects such as oxygen vacancies. So far, experiments have pegged an energy separation between these localized states and the Fermi level, while theory has predicted that these are in fact occupied states. To rationalize the defect-mediated potential tunnelling landscape, we have performed experiments in which we tune the MTJ’s Fermi level by altering one electrode’s work function. We find that switching the top electrode from FeCoB to FeB increases the amplitude of defect-mediated barrier heights. Ab initio theory attributes this increase to an increased energy separation between the localized states of single and double oxygen vacancies and the Fermi level. We thus extract a rationalized potential landscape of tunnelling across oxygen vacancies in MgO involving occupied states. In junctions with high R.A. product such as ours, this leads to a picture of hole tunnelling.