The origin of selectivity in protein hydrolysis promoted by Zr(IV)-substituted polyoxometalates (POMs) has been investigated through a variety of computational techniques. Initially, we analyzed the reaction mechanism for the observed hydrolysis at the Asn44-Arg45 site in hen egg-white lysozyme protein (HEWL) by Zr-substituted Lindqvist anion [W 5 O 18 Zr(H 2 O)(OH)] 3-(ZrL), using cluster models obtained from molecular dynamics (MD) simulations, quantum mechanics / molecular mechanics (QM/MM) calculations and metadynamics simulations. The mechanism characterization shows that the overall activity is governed by the energy cost to reach the transition state for C-N bond cleavage from reactants, resulting in a calculated, overall free-energy barrier of 121 kJ mol -1 , which is in excellent agreement with the values derived from experimental rate constants (113-134 kJ mol -1 ). In addition, QM/MM metadynamics simulations on the early stages of the mechanism revealed the formation of an exergonic, non-covalent POM•••protein complex at the protein surface stabilized by positively charged amino acids that are maintained during Zr coordination to amide oxygen. For non-reactive, related sites containing Arg (Asn113-Arg114, Arg45-Asn46, and Arg21-Gly22) we found very similar overall barriers within the cluster model approach (124, 124 and 120 kJ mol -1 , respectively); however their non-bonding POM•••protein interactions along the simulated coordination of Zr to the amide oxygen are significantly weaker than those for the reactive Asn44-Arg45 site. Thus, for HEWL protein the selectivity is governed by an enzyme-like recognition of the ZrL at the cleavage site that results in an overall acceleration of the reaction rate compared to other sites. Conversely, for human serum albumin (HSA) the observed selectivity is not directed by non-bonding POM•••protein interactions, but it is controlled by protein secondary structure. Calculations on several Arg-Leu sites placed in positive patches showed that peptide bonds in α-helix structure have higher overall free-energy barriers, while for the active Arg114-Leu115 site in a random coil region, the C-N cleavage is facilitated by the extended conformation of the protein chain. All in all, this study has identified and evaluated two complementary factors controlling the selectivity in peptide hydrolysis promoted by transition metal-substituted POMs; hydrolysis is disfavored at α-helical regions of protein, and then, specific positively charged patches can trap the POM via electrostatic-type POM•••protein interactions and accelerate the reaction.