The catalytic hydrolysis of the Gly-Pro substrate by the bimetallic prolidase active site model cluster has been investigated at the DF/B3LYP level of theory, in order to provide fundamental insights into the still poorly understood mechanism of prolidase catalysis. To date, the majority of prolidases exhibits metal-dependent activity, requiring two divalent cations such as Zn(2+), Mn(2+), or Co(2+) for maximal activity. In addition, it has been shown recently that two different metal ions in the active site of human prolidase (Zn and Mn) can coexist, with the protein remaining partially active. With the purpose of identifying which is the most efficient dimetallic center for the prolidase catalyzed reaction, Zn(II), Co(II), and Mn(II) have been examined as potential catalytic metals for this enzyme. Furthermore, to better elucidate the exact roles played by the metals occupying the site 1 and site 2 positions, the hetero-bimetallic active site having Zn and Mn cations has been also investigated, considering the two derivatives Mn1-Zn2 and Zn1-Mn2. The rate-determining step of the hydrolysis reaction is always found to be the nucleophilic addition of the hydroxide ion on the carbonyl carbon of the scissile peptide bond, followed by the less energetically demanding proline-peptide C-N bond scission. The analysis of the involved energy barriers does not indicate clearly a preference for a particular metal by the prolidase enzyme. Instead, we may point out a slightly better behavior of the cobalt-containing cluster as far as both tetrahedral formation and its decomposition are concerned, due to a greater degree of ligands-to-metals charge transfer. The mixed Mn-Zn hetero-dimetallic clusters appear to be also able to perform the hydrolysis of the Pro-Gly substrate, with a slight preference for the Mn1-Zn2 configuration.