New zircon U-Pb geochronology from a peridotite suite near Ranau and the Telupid ophiolite in Sabah, eastern Malaysia, contradict previous studies, which assumed that the Sabah mafic-ultramafic rocks are largely ophiolitic and Jurassic–Cretaceous in age. We show that these rocks formed during a magmatic episode in the Miocene (9.2–10.5 Ma), which is interpreted to reflect infiltration of melts and melt-rock reaction in the Ranau subcontinental peridotites during extension, and concurrent seafloor spreading forming the Telupid ophiolite further south. Older zircons from the Ranau peridotites have Cretaceous, Devonian, and Neoproterozoic ages. Zircon Lu-Hf isotopic data suggest their derivation from a depleted mantle. However, significant proportions of crustal components have been incorporated in their genesis, as evidenced by their less-radiogenic Hf signature compared to a pristine mantle reservoir. The involvement of a crustal component is consistent with our interpreted continental setting for the Ranau peridotite and formation in a narrow backarc basin for the Telupid ophiolite. We infer that the Sulu Sea, which was expanding throughout much of the Miocene, may have extended to the southwest into central Sabah. The Telupid oceanic strand formed during the split, collapse, and rollback of the Sulu arc due to the subduction of the Celebes Sea beneath Sabah. Incorporation of the Sulu arc in the evolving Miocene oceanic basin is a potential source to explain the involvement of crustal material in the zircon evolution of the Telupid ophiolite