Protector Shoal, the northernmost and most silicic volcano of the South Sandwich arc, erupted dacite–rhyolite pumice in 1962. We report geochemical data for a new suite of samples dredged from the volcano. Geochemically, the dredge and 1962 samples form four distinct magma groups that cannot have been related to each other, and are unlikely to have been related to a single basaltic parent, by fractional crystallization. Instead, the silicic rocks are more likely to have been generated by partial melting of basaltic lower crust within the arc. Trace element and Sr–Nd isotope data indicate that the silicic volcanics have compositions that are more similar to the volcanic arc than the oceanic basement formed at a back-arc spreading centre, and volcanic arc basalts are considered to be the likely source for the silicic magmas. The South Sandwich Islands are one of several intra-oceanic arcs (Tonga–Kermadec, Izu–Bonin) that have: (1) significant amounts of compositionally bimodal mafic–silicic volcanic products and (2) 6.0–6.5 km s−1P-wave velocity layers in their mid-crusts that have been imaged by wide-angle seismic surveys and interpreted as intermediate-silicic plutons. Geochemical and volume considerations indicate that both the silicic volcanics and plutonic layers were generated by partial melting of basaltic arc crust, representing an early stage in the fractionation of oceanic basalt to form continental crust.