In this study we present combined high-resolution records of sea surface temperature (SST), phytoplankton productivity, and nutrient cycling in the Benguela Upwelling System (BUS) for the past 3.5 Ma. The SST record provided evidence that upwelling activity off Namibia mainly intensified ca. 2.4–2.0 Ma ago in response to the cooling of the Southern Ocean and the resultant strengthening of trade winds. As revealed by productivity-related proxies, BUS intensification led to a major transition in regional biological productivity when considering the termination of the Matuyama Diatom Maximum (a diatom high-production event). Major oceanic reorganization in the Benguela was accompanied by nutrient source changes, as indicated by a new nitrogen isotopic (δ15N) record that revealed a stepwise increase at ca. 2.4 and ca. 1.5 Ma ago. The change in source region likely resulted from significant changes in intermediate water formation tied to the reorganization of oceanic conditions in the Southern Ocean, which may have in turn mainly controlled the global ocean N cycle, and therefore the N isotopic composition of nutrients since 3.5 Ma ago.