Understanding the interactions between soil bacteria, fungi, and nematodes in coffee agroecosystems is crucial for optimizing sustainable agriculture. This study investigated the composition and functional dynamics of these communities under conventional and sustainable management systems. Soil samples were collected from three major coffee-growing regions in Costa Rica, representing different agricultural regimes. Nematode community was analyzed using optical microscopy, while microbial communities were analyzed using high-throughput sequencing. In both cases, bioinformatic tools were used for functional prediction based on taxonomy.. Herbivorous nematodes dominated both systems, while bacterivores (Rhabditidae, Cephalobidae) and fungivores (Aphelenchoidae) were significantly more abundant in soils subject to sustainable practice (p < 0.05). Nematode maturity indices and food web diagnostics showed no significant differences between systems, even though metabolic footprints related to organic matter decomposition varied (p < 0.05). Bacterial communities were dominated by the phyla Proteobacteria, Acidobacteria, and Chloroflexi, while the fungal community was largely composed of Ascomycota (53.21% in both systems). The fungal genus Mortierella was particularly prevalent. Soil pH, along with Ca, Mg, K, and extractable acidity, influenced community composition. Functional profiles revealed higher gene abundances linked to nutrient and energy cycling in sustainable systems, particularly phosphorus and sulfur metabolism. Saprotroph-symbiotroph fungi were more common in sustainable soils, while pathotrophic fungi dominated conventional systems. This is the first comprehensive analysis of bacteria, fungi, and nematodes across different agricultural practices in coffee agroecosystems in Costa Rica.