Silica (Si) is of great concern to agronomists because it has a beneficial effect on plant resistance to various stresses, enabling yield optimization in economically important crop species. Yet biogenic silica (BSi) cycling in soils controls a large part of the Si export fluxes to rivers and oceans. Despite the importance of agricultural-harvest-related Si removal, previous studies have not addressed this topic thoroughly. By performing a detailed quantification of agricultural Si export in Western Europe's Scheldt River basin, we show that harvest not only disrupts BSi cycling but also introduces an agricultural Si pathway, with major export Si fluxes as compared with BSi production in climax forest communities and grasslands. Harvesting substantially changes terrestrial Si cycling because reconstitution of BSi to soils in litter fall is prevented. The agricultural Si loop clearly constitutes an important flow of BSi out of terrestrial ecosystems one that is currently unrecognized in global biogeochemical Si cycling.