Three types of zircon coexist in an unusual lower crustal xenolith from the Valle Guffari diatreme (Hyblean Plateau, Sicily): igneous Type 1 (near-euhedral, weakly zoned; Ce/Ce* > 1); partially recrystallised Type 2 (ovoid, structureless; weak Ce anomaly); hydrothermal Type 3 (sugary, spongy-textured, probably related to F-rich aqueous fluids). U–Pb dating by LAM-ICPMS, supported by in situ Hf-isotope analysis, suggests that both Type 1 and Type 2 zircons were originally Archean (ca 2.7 Ga), though many of these grains have experienced severe Pb loss. The U–Pb ages of the hydrothermal zircons cluster around 246 Ma, interpreted as the timing of the hydrothermal event. Their εHf (+ 8.5 to − 1.2) indicates the mixing of old crustal components and material from a juvenile source. In situ Os-isotope analyses of sulfides hosted in peridotite xenoliths from Valle Guffari show Paleoproterozoic–Archean TRD minimum ages, corresponding to the age of the oldest zircon grains in the crustal xenolith. Other peaks of TRD ages suggest that multiple metasomatic events have affected the lithospheric mantle. These observations suggest that the lower crust and the upper part of the lithospheric mantle beneath the Hyblean Plateau represent the northernmost portion of the African Plate. These two units have coexisted since at least late Archean time, and have remained linked through several episodes of crustal modification, including the Permo-Triassic hydrothermal event, which was probably related to the onset of rifting in the Ionian Basin.