In the Hellenides of northern Greece, the Kassandra–Sithonia and Central Chalkidiki ophiolites constitute the Vardar suture zone against the Serbo-Macedonian margin of Eurasia. The mafic-intermediate to acid members in the crustal section of the Kassandra–Sithonia ophiolites have N- and E-MORB signatures compatible with an origin in a back-arc spreading center. The MORB mantle source has received subduction zone input from the nearby Paikon arc system as revealed by LILE and LREE enrichments. A diorite from the Gerakini complex presumably belonging to the Central Chalkidiki ophiolites shows more enriched HFSE and REE patterns relative to MORB and Na-rich character compared to the Kassandra–Sithonia ophiolites. The Sithonia ophiolite crystallization spans from 159 to 149 Ma, and the Gerakini complex diorite crystallized at 173 Ma as derived from new U–Pb zircon geochronology. The main cluster of Permo-Carboniferous, a small cluster of Neoproterozoic–Cambrian and few Proterozoic, Ordovician, Devonian, Triassic and Middle Jurassic inherited zircons derive from the Serbo-Macedonian margin units. Thus, a Late Jurassic ca. 10 Ma lasting igneous accretion of the Kassandra–Sithonia back-arc crust within the eastern Vardar zone is now well constrained and corroborated by Berriasian–Early Valanginian supra-ophiolite cover limestones. Instead of an affinity to the Central Chalkidiki ophiolites, the Gerakini diorite exhibits chemical similarity to the Chortiatis arc magmatic suite of the Circum-Rhodope belt within the eastern Vardar zone. The Gerakini diorite predates the Sithonia ophiolite in which the Chortiatis arc suite supplied Middle Jurassic inherited zircons. The Chortiatis arc compared with arc-related Evros ophiolites of the Circum-Rhodope belt in Thrace region shows the same 173–160 Ma life span and tectonic setting, implying the extension of the arc systems across the north Aegean Sea. Based on these new temporal constraints, a tectonic scenario of Jurassic subduction settings and arc/back-arc systems development in the Maliac and Vardar oceanic basins is proposed that also accounts for continental magmatism in the Serbo-Macedonian margin of Eurasia.