This study reconstructs the upwelling history of the Southern Benguela Upwelling System (SBUS), examining its sensitivity to both regional and global climatic influences. We analyze planktic foraminiferal relative abundance and stable isotope data from ODP Site 1087 to investigate the history of SBUS since ∼ 6.1 Ma. During the latest Miocene-earliest Pliocene, the SBUS experienced increased productivity, fueled by wind-driven upwelling and an enriched global nutrient reservoir associated with the late Miocene biogenic bloom. The early Pliocene witnessed an apparent weakening of the SBUS due to the deepening of the global thermocline and weak trade winds. Significantly, our proxy records indicate strengthening of the SBUS beginning before the onset of intense northern hemisphere glaciation (iNHG) between 3.5 and 3 Ma. Despite contraction of upwelling cells after ∼ 3 Ma, our study challenges the notion of water column stability during the Matuyama Diatom Maximum event (3 to 2 Ma); we alternatively propose the existence of water column instability and probable presence of upwelling during this time. Post 2 Ma, the main upwelling cells shifted northward in response to the strengthening and equatorward migration of the Hadley cell, marked by long-term marginal upwelling. The SBUS achieved its modern state by ∼ 1 Ma with complete isolation from the coastal upwelling zone. Our observations indicate a strong correlation between the history of SBUS and global climatic events, with a strong correlation between them prior to the initiation of iNHG. Subsequently, local climatic influences have become more predominant, overshadowing the signals from global climatic events. The data also suggest linkages between shifts in the SBUS strengths and southwest African climate.