The hydrolysis of horse heart cytochrome c (cytC) protein by two isostructural Keggin‐type polyoxometalates (POMs), (Me2NH2)10[Ce(α‐PW11O39)2] (Ce1–K2) and (Et2NH2)10[Zr(PW11O39)2] (Zr1–K2), which differ in the nature of the embedded Lewis acid metal ion, has been investigated. In the presence of Ce1–K2, selective hydrolysis of cytC was observed at the Trp60‐Lys61 and Gly78‐Thr79 peptide bonds at pH 7.4 and 37 °C. However, the isostructural Zr1–K2 exhibited a lower reactivity and different selectivity, cleaving cytC at the Asp3‐Val4, Asp51‐Ala52 and Gly78‐Thr79 peptide bonds. Different spectroscopic techniques were used to verify the molecular interactions between cytC and each metal‐substituted Keggin POM to elucidate the role of the Lewis acid metal ion in directing the selectivity of protein hydrolysis.