Plant species differ greatly in their silicon (Si) uptake and accumulation, but little is known about the ecosystem Si cycling in species-rich tropical forest ecosystems. Here, we tested a hypothesis that patterns of Si cycling differ by elevation and bedrock on Mount Kinabalu. At eight permanent plots at four altitudes (700, 1700, 2700 and 3100m) on two geological substrates (non-ultrabasic and ultrabasic), we compared these plots for Si concentrations of live leaves of dominant trees (total relative basal area > 60%), leaf litter (collected from 20 traps per plot), and A-horizon soil. Leaf samples were analyzed after alkaline digestion (1% NaCO3) at 85°C, and soil Si availability was determined after shaking in water at room temperature. Si accumulating species were more common at lower elevation sites. Si concentration in leaf litter followed the community-level trend in live leaves. Si availability in soils increases at lower altitude sites on both bedrocks. In conclusion, ecosystem Si cycling is more active in lowland tropics compared to higher altitudes, suggesting that plants significantly modulate ecosystem Si cycling on Mt. Kinabalu and other tropical forests.