Primitive melt inclusions in chrome spinel from the Ogasawara Archipelago (Japan) compose two discrete groups of high-SiO2, high-MgO (high-Si) and low-SiO2, low-MgO (low-Si) boninitic suites, with ultra-depleted dish- and V-shaped, and less-depleted flat, rare earth element patterns. The most magnesian melt inclusions of each geochemical type were used to estimate the temperature-pressure conditions for primary boninites, which range from 1345 °C at 0.56 GPa to 1421 °C at 0.85 GPa for the 48–46 Ma low-Si and high-Si boninites, and 1381 °C at 0.85 GPa for the 45 Ma low-Si boninite. The onset of the Pacific slab subduction at 52 Ma forced upwelling of depleted mid-oceanic ridge basalt mantle (DMM) to yield proto-arc basalt (PAB). With the rise of DMM, refractory harzburgite ascended without melting. At 48–46 Ma, introduction of slab fluids induced melting of the PAB residue and high-temperature harzburgite, resulting in the low-Si and high-Si boninites, respectively. Meanwhile, convection within the mantle wedge brought the less-depleted residue of PAB and DMM into the region fluxed by slab fluids, which melted to yield the less-depleted low-Si boninite at 45 Ma, and fertile arc basalts, respectively.