The global late Pliocene/early Pleistocene cooling (~3.0-2.0 million years ago, Ma) concurred with extremely high diatom and biogenic opal production in most of the major coastal upwelling regions. This phenomenon was particularly pronounced in the Benguela Upwelling System (BUS), off Namibia, where it is known as the Matuyama Diatom Maximum (MDM). Our study focuses on a new diatom silicon isotope (δ³⁰Si) record covering the MDM in the BUS. Unexpectedly, the variations in δ³⁰Si signal follow biogenic opal content, whereby the highest δ³⁰Si values correspond to the highest biogenic opal content. We interpret the higher δ³⁰Si values during the MDM as a result of a stronger degree of silicate utilization in the surface waters caused by high productivity of mat-forming diatom species. This was most likely promoted by weak upwelling intensity dominating the BUS during the Plio/Pleistocene cooling combined with a large silicate supply derived from a strong Southern Ocean nutrient leakage responding to the expansion of Antarctic ice cover and the resulting stratification of the polar ocean 3.0-2.7 Ma ago. A similar scenario is hypothesized for other major coastal upwelling systems (e.g. off California) during this time interval, suggesting that the efficiency of the biological carbon pump was probably sufficiently enhanced in these regions during the MDM to have significantly increased the transport of atmospheric CO₂ to the deep ocean. In addition, the coeval extension of the area of surface water stratification in both the Southern Ocean and the North Pacific, which decreased CO₂ release to the atmosphere, led to further enhanced atmospheric CO₂ drawn-down and thus contributed significantly to late Pliocene/early Pleistocene cooling.