The Twyfelskupje carbonatite complex, Southern Namibia, exhibits the typical igneous emplacement structures of carbonatites, including plugs, cone sheets and dyke stockworks. The excellent exposure allows for detailed studies of the high-level geochemical and structural evolution of the carbonatite, and the nature of the concomitant rare earth element mineralization. Radiogenic isotope analyses (Sr, Nd, Pb) reveal that, in common with many other carbonatites, the Twyfelskupje carbonatite complex appears to be predominantly derived from mixing between HIMU and EM1 mantle end-members. Following partial melting of these mantle sources, the geochemical and structural evolution of the Twyfelskupje carbonatite complex proceeded by a staged process involving separate magma pulses, a series of emplacement structures, sub-solidus crystallization, fractionation and low-temperature hydrothermal alteration. The dominant rare earth element minerals in the Twyfelskupje carbonatite complex are fluorcarbonates and monazite, and are characterized by variable Ca, high F and light rare earth elements in the order Ce>La>Nd. Comparison between the rare earth element concentrations of the whole rocks, dominant rare earth element minerals and carbonates suggests that ∼95 % of the total rare earth element abundance of the Twyfelskupje carbonatite complex is contained within fluorcarbonates and monazite. Overall, the early calcio-carbonatite plugs are rare earth element enriched (mean 4.47 wt % rare earth oxides) relative to the magnesio-carbonatite cone sheets (mean 2.51 wt % rare earth oxides).