Ferns (Polypodiophyta) are an abundant floral element of the tropics with high sensitivity to environmental conditions and good indicators of overall biodiversity. Here, we set out to identify which geochemical factors determine fern diversity in a low-montane tropical rainforest in Eastern Ecuador. We conducted a field survey of high-spatial resolution completing a comprehensive fern inventory across two elevational ranges, combined with biochemical characterisation of the underlying soils. While α-diversity was negatively correlated with cation exchange capacity (CEC) and with elevation, β-diversity increased with elevation and with geographic distance, as predicted. Our results confirm that ferns have a high sensitivity to both elevational and environmental gradients, where the latter in this study was derived from enhanced aluminium, iron and calcium contents in some of the studied soils. Further monitoring of fern communities could therefore help to better understand and predict how environmental change may impact biodiversity, with a particular focus on threats potentially arising from toxic elements being released in tropical soils through modified soil CEC.