Understanding the protonation behavior of metal-oxo water oxidation catalysts is essential to improve catalyst efficiency and long-term performance, as well as to tune their properties for specific applications. In this work, we explore the basicity and protonation effects of the highly active water oxidation catalyst [(Mn4O4) (V4O13) (OAc)3]3- using density functional theory. We computed the relative free energies of protonation in a systematic fashion for all symmetry-inequivalent O atoms, where the presence of multiple oxidation states from Mn4IV to Mn4III and a rich Jahn-Teller isomerism adds a significant amount of complexity. For high oxidation states, the compound behaves like some other polyoxometalates, showing protonation preferably at the terminal and μ2-bridging O atoms of the vanadate cap. However, upon reduction, eventually, the protonation preference switches to the cubane O atoms, mostly driven by a strong increase in basicity for O atoms located along the Jahn-Teller axes. Our work further evidences that protonation can potentially lead to several chemical transformations, like disproportionation and charge transfer to vanadium, dissociation of ligands, or the opening of the cubane structure. Our simulated UV/Vis absorption spectra additionally provide valuable insights about how the protonation of the catalyst could be tracked experimentally. Overall, our analysis highlights the complexity involved in the protonation of heterometallic polyoxometalate clusters.