Productive eastern boundary upwelling systems (EBUs) are characterized by abundant siliceous algae and diatoms, and they play a key role in carbon fixation. Understanding past shifts in diatom production is critical for predicting the impact of future climate change. We combine existing sediment archives from the Benguela EBU with new diatom isotope analyses and modelling to reconstruct late Quaternary silica cycling, which we suggest depends on both upwelling intensity and surface utilization.