Increased nutrient supply can have drastic effects on natural ecosystems, especially in naturally nutrient-poor ones such as most tropical rainforests. Many studies have focused on the reaction of trees to fertilization, but little is known about herbaceous plants. Ferns are a particularly common group in tropical forests, spanning all vegetation types and zones. Here, we assess how seven years of moderate addition of nitrogen (N), phosphorus (P), and N+P along an elevational gradient (1000–3000 m) have impacted richness and composition of fern and lycophyte assemblages in tropical montane rain forests growing on naturally nutrient deficient soils in the Ecuadorian Andes. We found that fertilization does not affect overall species richness, but that there were strong differences in species abundances (∼60% of species), both negative and positive, that were apparently related to the systematic affiliations and ecological properties of the affected species. These diverse responses of ferns to fertilization provide insight into the sensitivity and complexity of the relationships of nutrient availability and community composition in tropical forests.