The Manihiki Plateau, a Large Igneous Province (LIP) in the western Pacific, has been proposed to be emplaced as part of the “Greater Ontong Java Event” during the early Cretaceous. Shortly after its formation, the Manihiki Plateau fragmented into multiple sub-provinces. Plate tectonic reconstructions ignore this fragmentation, treating the Manihiki Plateau as a single crustal block. By analyzing two seismic refraction/wide-angle reflection profiles crossing the two largest sub-provinces of the Manihiki Plateau, we provide new insight into their deep crustal structure and magmatic evolution. Our data indicate that the High Plateau and the Western Plateaus were emplaced as a single unit during an initial phase of massive magmatic activity, but later magmatic stages altered the individual sub-provinces considerably. The High Plateau has a crustal thickness of 20 km and its P-wave velocity distribution is comparable to previously surveyed oceanic LIPs. Strong secondary magmatic phases are visible by eruptive centers and former magmatic pathways in the middle and lower crust. The Western Plateaus, which have a crustal thickness decreasing gradually from 17.3 km (East) to 9.2 km (West), experienced smaller amounts of magmatism mainly along fault zones and on local seamounts. Therefore, we propose a distinct development of the two main sub-provinces of the Manihiki Plateau after their initial joint emplacement. The High Plateau experienced voluminous multi-phase magmatic accretion and extrusion, whereas the thinner Western Plateaus exhibit only relatively minor magmatic growth. Such a large difference in the evolution process has not been reported from any other oceanic LIP so far.