Abstract Sakurajima volcano has developed since 26 ka through post-caldera magmatic activity at the Aira caldera (formed at 30 ka) and is one of the most active volcanoes in Japan. In this study, new petrological and geochemical analyses were conducted on proximal volcanic products to understand the origin and evolution of the magmatic system during the Holocene. The volcanic products have andesitic and dacitic compositions (58–69 wt.% SiO2), and relatively older products (9–1.6 ka) and younger products (<1.3 ka) are characterised by having lower and higher P2O5 contents, respectively (low- and high-P2O5 groups, respectively). The low-P2O5 group products had lower TiO2 and Y contents, higher 87Sr/86Sr, 206Pb/204Pb, 207Pb/204Pb, and 208Pb/204Pb ratios, and lower 143Nd/144Nd ratios than the high-P2O5 group products. It is suggested that the low-P2O5 group magmas were produced by the partial melting of lower crustal materials, and the compositional variations primarily reflected the variation in the degree of melting, with some contribution from mixing with mafic magmas. In contrast, the high-P2O5 group magmas were produced by mixing mafic and felsic magmas in varying proportions. The mafic end-member magmas evolved from mantle-derived primitive magmas with some contribution from crustal assimilation. The felsic end-member magmas were produced by fractional crystallisation following the melting of lower crustal materials with higher melting degrees than those of the low-P2O5 group magmas. In summary, the geochemical evolution of Holocene magmatic activity at Sakurajima was essentially controlled by intermittent discharges of partial melts from the lower crustal source region with increasing melting degrees. The remnants of the voluminous Aira rhyolitic magmas from caldera-forming eruptions were not involved in the Holocene magmatic system. Lower crustal source materials that produced the Aira rhyolites were also not involved. The lower crustal melting region, which was the main source of Holocene magmatism at Sakurajima, may have already existed at ~100 ka, well before the caldera-forming eruption at 30 ka.