The Dun Mountain ophiolite, South Island, New Zealand, records complex overprinting of mantle fabrics. Using structural observations, microstructural analysis, geothermometry, geobarometry, geochronology and rheological constraints from the Red Hills and Dun Mountain massifs, we propose that three deformation events occurred during the early stages of subduction initiation along the Permian margin of Gondwana. During the first deformation event, the lineated Two Tarns Harzburgite from the Red Hills formed in a transtensional setting associated with subduction initiation. Deformation was pervasive, homogeneous and simultaneous with boninitic melt migration through the unit; it also occurred at very fast strain rates (10−9–10−8 s−1). During the second deformation event, progressive exhumation to c. 5 kbar and cooling to 1000°C led to the localization of melt and deformation into distinct zones (Dun Mountain, and the Plateau Complex, Plagioclase Zone and Ellis Stream Complex of the Red Hills). The third deformation event resulted in continued cooling and exhumation along serpentinized faults. This history provides a rare glimpse of the coupled fabric development and melt migration that sequentially develop in the early mantle wedge during the initiation of a subduction zone.