Zircons recovered from oceanic gabbro exposed on Atlantis Bank, Southwest Indian Ridge, typically display oscillatory and sector zoning consistent with igneous crystallization from mafic magmas. In one rock (of twenty investigated), weak-oscillatory-zonation patterns are overprinted by secondary textural features characterized by mottled, convoluted and wavy internal zonation patterns that are frequently associated with secondary micron- to submicron-scale micro-porosity. These zircons are hosted in a felsic vein that intruded an oxide gabbro, both of which are cross-cut by monomineralic amphibole- and quartz-rich veinlets. Zircons with weak-oscillatory-zonation patterns record a weighted-average ²⁰⁶Pb/²³⁸U age of 12.76 ± 0.20 Ma (mswd = 1.5), and have high trace element concentrations [e.g., ΣREEs (∼ 0.4–2.2 wt.%), Y (∼ 0.6–2.8 wt.%), P (∼ 0.4–0.9 wt.%)], and Th/U (0.1–0.5). These zircons are anomalously old (≥1 Myr) relative to the magnetic age for this portion of oceanic crust (11.75 Ma). In contrast, zircons with non-igneous, secondary textures have a younger weighted-average ²⁰⁶Pb/²³⁸U age of 12.00 ± 0.16 Ma (mswd = 1.7), and have lower trace element concentrations [e.g., ΣREEs (∼ 0.2–0.8 wt.%), Y (∼ 0.3–1.0 wt.%), P (∼ 0.1–0.3 wt.%)], and slightly lower Th/U (0.1–0.3). The weighted-average age of these zircons is similar to the magnetic anomaly age, and other ²⁰⁶Pb/²³⁸U ages of nearby rocks. We do not observe a correlation between crystallographic misorientation, internal texture, or trace element chemistry. We suggest that the decrease in trace element concentrations associated with the development of non-igneous alteration textures is attributed to the purging of non-essential structural constituent cations from the zircon crystal lattice at amphibolite-facies conditions. The mechanism of alteration/re-equilibration was likely an interface-coupled dissolution–reprecipitation processes that affected pre-existing, anomalously old zircons during shallow-level magmatic construction of Atlantis Bank at ∼ 12.0 Ma.