The initiation of tectonic plate subduction into the mantle is poorly understood. If subduction is induced by the push of a distant mid-ocean ridge or subducted slab pull, we expect compression and uplift of the overriding plate. In contrast, spontaneous subduction initiation, driven by subsidence of dense lithosphere along faults adjacent to buoyant lithosphere, would result in extension and magmatism. The rock record of subduction initiation is typically obscured by younger deposits, so evaluating these possibilities has proved elusive. Here we analyse the geochemical characteristics of igneous basement rocks and overlying sediments, sampled from the Amami Sankaku Basin in the northwest Philippine Sea. The uppermost basement rocks are areally widespread and supplied via dykes. They are similar in composition and age—as constrained by the biostratigraphy of the overlying sediments—to the 52–48-million-year-old basalts in the adjacent Izu–Bonin–Mariana fore-arc. The geochemical characteristics of the basement lavas indicate that a component of subducted lithosphere was involved in their genesis, and the lavas were derived from mantle source rocks that were more melt-depleted than those tapped at mid-ocean ridges. We propose that the basement lavas formed during the inception of Izu–Bonin–Mariana subduction in a mode consistent with the spontaneous initiation of subduction.