A recent study [Angew. Chem. Int. Ed. 2015, 54, 7391–7394] has shown that horse heart myoglobin (HHM) is selectively hydrolyzed by a range of zirconium(IV)-substituted polyoxometalates (POMs) under mild conditions. In this study, the molecular interactions between the Zr-POM catalysts and HHM are investigated by using a range of complementary techniques, including circular dichroism (CD), UV/Vis spectroscopy, tryptophan fluorescence spectroscopy, and 1H and 31P NMR spectroscopy. A tryptophan fluorescence quenching study reveals that, among all examined Zr-POMs, the most reactive POM, 2:2 ZrIV-Keggin, exhibits the strongest interaction with HHM. 31P NMR spectroscopy studies show that this POM dissociates in solution, resulting in the formation of a monomeric 1:1 ZrIV-Keggin structure, which is likely to be a catalytically active species. In the presence of ZrIV-POMs, HHM does not undergo complete denaturation, as evidenced by CD, UV/Vis, tryptophan fluorescence, and 1H NMR spectroscopy. CD spectroscopy shows a gradual decrease in the α-helical content of HHM upon addition of ZrIV-POMs. The largest effect is observed in the presence of a large ZrIV-Wells–Dawson structure, whereas small ZrIV-Lindqvist POM has the least influence on the decrease in the α-helical content of HHM. In all cases, the Soret band at λ=409 nm is maintained in the presence of all examined Zr-POMs, which indicates that no conformational changes in the protein occur near the heme group.