The Benguela Upwelling System (BUS), located between 30 and 20°S, is one of the fundamental high-productivity systems of the world ocean. The BUS has previously been studied in terms of primary productivity and ecology over glacial-interglacial timescales; however, the response and coupling with the benthic environment have received little attention. Here, for the first time, we present a high-resolution reconstruction of the BUS highlighting the link between surface and benthic productivity and their response to climatic and oceanographic changes over the last 70 ka. The study is based on benthic foraminiferal faunal analysis together with analyses of diatom assemblages, grain size of the terrigenous fraction, and stable O and C isotopic and bulk biogenic components of core GeoB3606-1. We reveal significant shifts in benthic foraminiferal assemblage composition. Tight coupling existed between the surface and bottom water environment especially throughout marine isotope stages 4 and 3 (MIS4 and MIS3). Due to the high export production, the site has essentially experienced continuous low oxygen conditions; however, there are time periods where the hypoxic conditions were even more notable. Two of these severe hypoxic periods were during parts of MIS4 and MIS3 where we find an inverse relationship between diatom and benthic foraminifera accumulation, meaning that during times of extremely high phytodetritus export we note strongly suppressed benthic productivity. We also stress the importance of food source for the benthos throughout the record. Shifts in export productivity are attributed not only to upwelling intensity and filament front position, but also, regional-global climatic and oceanographic changes had significant impact on the BUS dynamics.