A petrographic study of “Verde Prato” (trade name of an ophiolitic serpentinised peridotite quarried in Tuscany) revealed, next to a relict Cr-spinel, another opaque ore mineral apparently containing ca.17 wt% SiO2. In order to unveil the origin of this anomalous composition, detailed SEM-EDS, μ-Raman spectroscopy and X-ray microdiffraction investigations were undertaken, which provided useful but somehow contrasting indications. Therefore, in order to definitely unveil the nature of the unusual opaque mineral, a specific TEM study was undertaken. This showed the presence of submicroscopic euhedral Mn-Cr-Fe-spinels in a matrix of a 7 Å layer-silicate (Al-lizardite). Interesting, all the submicroscopic spinel grains were found to share the same crystallographic orientation, suggesting an origin from a single, larger, former crystal. This unusual type of alteration of the mantle spinel probably occurred on the ocean floor during the pervasive polyphase process of hydrothermal peridotite serpentinization. Overall, by mapping the different serpentinite microstructures and compositions, a polyphase serpentinization history consisting of at least eight different cycles has been suggested. Moreover, the spinel composition indicates that the alteration was accompanied by Mn-metasomatism, made possible by the close proximity of Mn-rich hydrothermal vents, such as “black smokers”.