The Archaean continental crust comprises two major groups of silicon-rich granitoids: the tonalite–trondhjemite–granodiorite and granite–monzonite–syenite suites, which differ in their sodium-to-potassium ratios. How these felsic granitoids evolved from their mafic precursors remains elusive and the subject of great debate. Here, we present silicon isotopic constraints on the formation of representative trondhjemitic and granitic plutons from the Kaapvaal craton that range in age from 3.51–2.69 billion years ago. We identified very consistent silicon isotopic signatures, all uniformly 0.1–0.2‰ heavier than rocks of the modern continental crust. This unusual composition is explained by the melting of a mafic source that included significant proportions (15–35 wt%) of silicified basalts, which were common supracrustal rocks before 3 billion years ago. Before the melting event that formed the granitoid magmas at depth, portions of the mafic source rocks were enriched in silica by interaction with silica-saturated seawater. The addition of silica depresses the stability of amphibole at similar water activity, allowing trondhjemitic and granitic melt production at lower temperatures from protoliths with contrasting silica contents: 52–57 and ≥60 wt%, respectively. This explains why granitoids were able to form very early in Earth history but did not emerge in significant amounts on other rocky planets.