This article presents data regarding the Si biogeochemical cycle during two oceanographic cruises conducted in the Southern Tropical Pacific (BIOSOPE and OUTPACE cruises) in 2005 and 2015. It involves the first Si stock measurements in this understudied region, encompassing various oceanic systems from New Caledonia to the Chilean upwelling between 8 and 34°S. Some of the lowest levels of biogenic silica standing stocks ever measured were found in this area, notably in the Southern Pacific Gyre, where Chlorophyll a concentrations are most depleted worldwide. Integrated biogenic silica stocks are as low as 1.08±0.95mmolm−2, and are the lowest stocks measured in the Southern Pacific. Size-fractionated biogenic silica concentrations revealed a non-negligible contribution of the pico-sized fraction (<2–3µm) to biogenic silica standing stocks, representing 26±12% of total biogenic silica during the OUTPACE cruise and 11±9% during the BIOSOPE cruise. These results indicate significant accumulation in this size-class, which was undocumented for in 2005, but has since then been related to Si uptake by Synechococcus cells. Our Si kinetic uptake experiments carried out during BIOSOPE confirmed biological Si uptake by this size-fraction. We further present diatoms community structure associated with the stock measurements for a global overview of the Si cycle in the Southern Tropical Pacific.