Abstract The Bandombaai Complex (southern Kaoko Belt, Namibia) consists of three main intrusive rock types including metaluminous hornblende- and sphene-bearing quartz diorites, allanite-bearing granodiorites and granites, and peraluminous garnet- and muscovite-bearing leucogranites. Intrusion of the quartz diorites is constrained by a U–Pb zircon age of 540±3 Ma. Quartz diorites, granodiorites and granites display heterogeneous initial Nd- and O isotope compositions ( ε Nd (540 Ma)=−6.3 to −19.8; δ 18O=9.0–11.6‰) but rather low and uniform initial Sr isotope compositions ( 87Sr/ 86Sr initial=0.70794–0.70982). Two leucogranites and one aplite have higher initial 87Sr/ 86Sr ratios (0.70828–0.71559), but similar initial ε Nd (−11.9 to −15.8) and oxygen isotope values (10.5–12.9‰). The geochemical and isotopic characteristics of the Bandombaai Complex are distinct from other granitoids of the Kaoko Belt and the Central Zone of the Damara orogen. Our study suggests that the quartz diorites of the Bandombaai Complex are generated by melting of heterogeneous mafic lower crust. Based on a comparison with results from amphibolite-dehydration melting experiments, a lower crustal garnet- and amphibole-bearing metabasalt, probably enriched in K 2O, is a likely source rock for the quartz diorites. The granodiorites/granites show low Rb/Sr (<0.6) ratios and are probably generated by partial melting of meta-igneous (intermediate) lower crustal sources by amphibole-dehydration melting. Most of the leucogranites display higher Rb/Sr ratios (>1) and are most likely generated by biotite-dehydration melting of heterogeneous felsic lower crust. All segments of the lower crust underwent partial melting during the Pan-African orogeny at a time (540 Ma) when the middle crust of the central Damara orogen also underwent high T, medium P regional metamorphism and melting. Geochemical and isotope data from the Bandombaai Complex suggest that the Pan-African orogeny in this part of the orogen was not a major crust-forming episode. Instead, even the most primitive rock types of the region, the quartz diorites, represent recycled lower crustal material.