A major outstanding question concerning the Bushveld Complex of South Africa is the genetic relationship between the granites (Lebowa Granite Suite, LGS) and granophyres (Rashoop Granophyre Suite, RGS), and their relation to the underlying layered mafic-ultramafic intrusion (Rustenburg Layered Suite, RLS). Here, we present new bulk rock major and trace elements, as well as Nd and Hf isotopes for 35 samples from the LGS (Nebo Granite) and RGS (Stavoren Granophyre and Zwartbank Pseudogranophyre) and combine this with published data to form a comprehensive dataset. The LGS and RGS range from ferroan to peraluminous compositions. Relative to the bulk continental crust, the granite and granophyres are depleted in Sc, V, Ti, P, Cr, and Sr, and either similar or enriched in other trace elements. εHf and εNd values (at 2055 Ma) show narrow ranges between −9.1 ± 0.8 to −6.8 ± 0.7 and − 6.0 ± 0.3 to −5.1 ± 0.6, respectively, across hundreds of kilometres, although higher εNd values have been reported previously (up to +5.2). These isotopic compositions correspond to published values for the RLS. Thus, the major element and isotopic composition as well as general trace element trends observed for LGS and RGS are consistent with derivation through fractional crystallization of basaltic magmas. A Rayleigh fractionation model for trace elements and major element mass balance suggest that c. 20% granite can be produced from fractional crystallization of such magmas. Multiple lines of evidence suggest that the granitic magmas mainly evolved in underlying, staging magma chambers rather than in the RLS chamber itself. This includes evidence for magma mixing in a newly identified transition zone separating RLS and LGS, the finding of zircon antecrysts in LGS and RGS, and the replenished and tapped nature of the RLS chamber.