Sediments of the continental shelf anoxic zones of the Benguela upwelling system (BUS) and the Peruvian upwelling system are present-day hotspots of trace element accumulation. However, contribution of the lithogenic trace element fraction and early diagenetic transformation processes are poorly constrained. The identification of source and accumulation mechanisms is necessary for the validation of trace elements as proxies for productivity and redox cycling, notably in highly dynamic upwelling systems such as the BUS. Here, we analyzed redox- and biosensitive elements (U, Ba, Ni), lithogenic tracers (Al, Ti, Zr), total organic carbon (TOC) and P in eleven short sediment cores from the Namibian shelf (ca. 22–25°S) as well as grain size fractionated hinterland samples from the Tsauchab Valley at Sossusvlei (∼25°S). These samples help to constrain the lithogenic trace element contributions, a prerequisite for a realistic interpretation of marine authigenic trace element data. Our findings corroborate previous findings that Zr is a sensitive tracer of the coarse fraction in marine sediment for dust input and/or sediment reworking. Hence, the combined analysis of the coarse fraction (Zr), organic matter, and P enrichments (TOC/P) differentiates between a calm, organic matter-rich central shelf environment and a more energetic phosphorite-rich southern shelf environment. A significant correlation of U with P in cores from the southern shelf corroborates previous findings of U incorporation into apatite, the initial formation of which requires oscillating oxic to sulfidic redox conditions. Non-apatite associated U dominates in the cores from the central shelf, where it is only enriched in the buried, anoxic parts of the sediment. This also supports oscillating oxic to sulfidic redox conditions in surface sediment, where U may be recycled. Hence, U accumulates either (i) in apatite under oscillating oxic to sulfidic conditions or (ii) in buried anoxic sediment sections. This strongly questions the use of U as indicator of suboxic conditions but rather anoxic conditions. While lithogenic fractions of U were negligible, the lithogenic fractions of Ba and Ni were found to be elevated. The calculation of authigenic Ba when accounting for lithogenic Ba from the Sossusvlei fine fractions gives more realistic authigenic Ba values. The high Ba enrichment in the BUS is interpreted as uptake of Ba by diatoms and/or nucleation of barite in P-rich diatom remains, as suggested previously. Given the shallow water depth of the cores, barite formation must already take place in subsurface waters (<50 m water depth) as opposed to previous suggesting greater water depths. The lithogenic background of Ni strongly varies from 23°S to 25°S based on Sossusvlei data and the literature. When authigenic Ni contents are calculated accordingly and plotted versus TOC, more systematic trends are seen (compared to total Ni versus TOC). Essentially all cores show an increase in the authigenic Ni/TOC ratio with sediment depth suggesting better preservation and retention of Ni as compared to TOC consistent with previous observations in sediments from the Peruvian upwelling system. This trend corroborates the use of Ni as a productivity indicator for upwelling sediments.