The molecular interactions of the Keggin polyoxometalate [Me₂NH₂]₁₀[Ce(PW₁₁O₃₉)₂] (1), which promotes selective hydrolysis of hen egg white lysozyme (HEWL) under physiological conditions, were investigated in detail by isothermal titration calorimetry (ITC), ³¹P NMR and circular dichroism (CD) spectroscopy. ITC experiments showed that mixing of 1 and HEWL at pH 7.4 and 25 or 37 °C resulted in complexes having 1 : 1 and 2 : 1 POM : HEWL stoichiometries, respectively, and thermodynamic profiles are in agreement with binding in the vicinity of the Trp28–Val29 and Asn44–Arg45 peptide bonds, which were previously shown to undergo selective hydrolysis by 1. Mixing of HEWL with (NH₄)₄Ce(SO₄)₄·4H₂O salt indicated the absence of any binding accentuating the importance of the polyoxometalate scaffold for selective interaction with the HEWL surface. In contrast, the lacunary Na₉[A-α-PW₉O₃₄] polyoxometalate showed an increased binding stoichiometry as compared to 1. Increasing the ionic strength resulted in thermodynamic signatures which indicate preservation of the interaction at the Trp28–Val29 site, while interaction at the Asn44–Arg45 appears disrupted due to competition with the salt ions. Decreasing the pH to 4.4 at 37 °C resulted in energetic contributions which suggest that binding at the Trp28–Val29 site is favored, while more pronounced binding at the Asn44–Arg45 site was anticipated when the pH was increased to 9.2. The absence of binding between 1 and α-lactalbumin (α-LA), a protein which is highly isostructural to HEWL but with an overall negative charge, was confirmed at pH 7.4 and 37 °C. The influence of the pH on the binding between 1 and α-LA was investigated, demonstrating that at lower pH values, where α-LA becomes more positively charged, a 1 : 1 interaction with 1 is observed.