Siliceous plankton is the main producer of marine primary production. Transport of their postmortem siliceous skeletons down to the sea floor is an obligatory course to keep the dynamic balance of marine silica cycling. Because siliceous microfossils record the variation of paleoceanographic primary productivity and its spatial and temporal distribution, biogenic silica has been a significant proxy for paleoenvironmental reconstruction. Here I review the early diagenesis of biogenic silica and its main controlling factors during the processes of sinking through water column and upper sediment burial, which will be instrumental in a comprehensive understanding of its major advances that have been performed within the last decades.