Listwaenitization processes have significantly altered the mantle section of the West Chalkidiki ophiolites, generating the second largest magnesite deposit in Greece. Although research studies have been conducted in the region, the post-magmatic processes, and especially the geotectonic settings under which listwaenitization took place, remain unclear. In this study, minerals and rocks were studied applying XRD, clay fraction, SEM, EMPA, ICP-MS, INAA, LA-ICP-MS, and thermodynamic modeling. The results revealed that alteration processes significantly affected the mantle wedge peridotite protoliths leading to the following chemical changes (a) SiO2 increase with decreasing MgO, (b) Cs, Pb, As, and V enrichments, (c) limited alteration of magnesiochromite hosted within listwaenitized chromitites and (d) enrichment in PPGE and Au in listwaenitized chromitites and desulfurized laurite. Alteration was induced by fluids deriving from subducted Mesozoic sediments, represented by the Prinochori Formation or chemically similar formations. The final product of completely silicified peridotite (silica listwaenite) is thermodynamically stable in Earth-surface conditions, with dolomite and phyllosilicates transforming into clay minerals. Based on detailed petrographical observations, peridotites were subjected to serpentinization, and subsequently, serpentine interacted with CO2, silica and calcium-bearing fluids, leading to its transformation into amorphous rusty-silica mass and/or tremolite.