Lowland tropical forests cycle a large amount of silicon (Si) via litter, but little is known about the effect of logging on Si cycling. Here, we aimed to understand Si cycling patterns in three lowland tropical forests that differed by past logging intensity (old growth, OG; reduced-impact logged, RIL; conventionally logged, CL) in Borneo. We collected dead leaves from dominant canopy tree species, litterfall for one year and surface soil samples (A- and AB-horizons). We measured Si in plant samples extracted in 1% Na₂CO₃ at 85°C and water-soluble Si in soil extracted by shaking in distilled water at room temperature. RIL and CL showed higher annual litter Si flux per unit ground area than OG, which was largely contributed by bamboo litter. Loss of dipterocarp species with high Si accumulation in OG was compensated by increased abundance of pioneer species with high Si leaf concentrations, such as Macaranga species, in RIL and CL. Water-extractable Si content in soil was higher in RIL and CL than in OG, following the trend of annual litter Si flux. These results suggested that logging should significantly influence biogeochemical Si cycling in Bornean lowland tropical forests when bamboo and other Si accumulating species become abundant.