The Hohonu Batholith is an aggregation of mostly mid-Cretaceous granitoid plutons on the West Coast of the South Island of New Zealand emplaced during a transitional period between subduction-related compression and continental lithospheric extension. This study reports an integrated dataset, comprising in-situ U-Pb, O and Hf isotope compositions and REE, Ti and other trace and major elements (Zr-Hf, Th-U) for zircons extracted from four representative plutons within the batholith. Our results provide detailed insight into the protracted thermal, chronological and geochemical histories. LA-ICPMS U-Pb zircon ages indicate a primary episode of magma genesis and emplacement from 107 to 113 Ma, confirming published SIMS dating. However, a younger previously unrecognized age population of ∼91–96 Ma is identified, primarily (although not exclusively) in zircon rims. This younger age event coincides with the timing of protracted lithospheric extension and crustal thinning of the Zealandia continent. The cryptic younger zircon ages suggest that Hohonu granitoids experienced a partial thermal overprint (accompanied by Pb loss) mostly recorded in rims. Differences in bulk rock geochemistry between plutons are inferred to reflect variable conditions of partial melting controlled by source mineralogy and H2O content. Isotope and trace element compositions, along with Ti-thermometry, measured on the same micro-volume of CL-imaged zircons, are used to test if source characteristics were imparted from melt to minerals in zircon-saturated silicic systems. Similarities are revealed in the zircon record of the selected plutonic rocks, confirming their broadly consanguineous relationship and the fundamental role of open-system behaviour, involving hybridization or assimilation between mantle-derived (or juvenile mafic) and crustal-derived components, as previously inferred from whole rock Nd-Sr isotope systematics. However, intra-sample decoupling of zircon O-Hf isotope systematics may also be linked to residual source unmixing. This possibility, in addition to mafic recharge, may have obscured melt source compositional characteristics, and hence zircon REE appear as unsuitable fingerprints of source(s) and conditions of partial melting in this granitoid system. Simple compositional and thermal magma evolution trends appear punctuated by episodes of mafic recharge, presumably during lithospheric thinning.