Silicon is an essential nutrient for marine diatoms, which dominate the export of organic carbon to the deep ocean. Despite the dominance of the oceanic Si budget by fluvial inputs and the role of the land biosphere in controlling Si losses from rocks and soils to rivers, few studies have considered how continental biogeochemical Si fluxes varied on an orbital timescale. We reconstruct changes in Si cycling by the catchment-lake ecosystem of Lake Rutundu, Mt Kenya (3078 m a.s.l.), over the last ca. 38 ka, using a novel combination of lake-sediment fluxes and stable-isotope (13C, 15N, 18O, 30Si) data. Under glacial conditions (38.3-14.3 ka BP), high diatom productivity was maintained by substantial losses of dissolved SiO2 and soil nutrients from a sparse, leaky, terrestrial ecosystem. During the following period of enhanced monsoon rainfall and seasonality (14.3-9.5 ka BP), rapid Si cycling by fire-prone, mesic grassland was associated with substantial aeolian transport of opal phytoliths by smoke plumes, but greatly reduced nutrient losses in runoff. Invasion of tall, subalpine shrubs after 9.5 ka BP further enhanced landscape stability, leading to very low sediment fluxes of both phytoliths and diatoms. This case study offers new insights into processes that may have operated at biome to continental scales during the late Quaternary.