Different forest systems can influence the function, traits, diversity, and distribution of ferns. By comparing ferns based on their functional traits, we can explore how species loss affects functional diversity, and consequently alter the forest ecosystem. We investigated the impact of abandoned silviculture on fern diversity (taxonomic and functional) and abundance. Our hypothesis suggests a positive effect of nutrients and soil humidity in native forests, while canopy openness in silviculture has a negative effect on monilophyte diversity. This study was conducted in three sites of native forest and three sites of Pinus silviculture. Each site was subdivided into three areas, with three plots per area, resulting in 54 plots (3 sites × 3 areas × 3 plots × 2 forest types). Each plot covered an area of 100 m2 (10 m × 10 m; 5400 m2 in total). In each plot, we estimated abundance, functional attributes (richness, evenness, divergence, and dispersion) based on leaf thickness, leaf width, petiole length, stem length, leaf division, sori shape, indusium presence, and taxonomic diversity. Results indicate that native forest exhibit higher taxonomic and functional diversity (richness—Fric) compared to abandoned Pinus plantations, which may be attributed to high habitat diversity and species specialization in specific microhabitats. In silviculture, diversity homogenization leads to an increase in the redundancy of functional attributes (evenness—Feve), resulting in the filtering out of similar organisms. Abiotic factors such as light and canopy openness negatively influence plant establishment and growth, leading to a decrease in leaf division and indusium presence/absence (by CWMs), supporting niche complementarity theory in natural forest and mass ratio theory in silviculture. Our findings highlight the enduring negative impact of silviculture, even after 20 years, on both the taxonomic and functional diversity of monilophytes, underscoring the crucial role of native forests in preserving fern diversity.