We explored the relationships between synthetic fertilizer use, yield, and ecosystem services in a coffee agroecosystem in the Tarrazú region in the central highlands of Costa Rica. Working in nine farms ranging from 0.3 to 2.7 ha in the CoopeTarrazú farmers' cooperative, we focused on two important indicators of ecosystem services: biological control agents and mycorrhizal fungi. Biological control agents (especially parasitoid wasps) are essential for population regulation of herbivorous arthropods that reside in coffee agroecosystems. Mycorrhizal fungi contribute to plant nutrition and disease resistance and produce a highly stable protein, glomalin, which is critical for soil aggregation. Soil aggregates hedge against erosion, particularly in sloping soils, by improving porosity. Slopes in this study ranged from 4% to 66%. We manipulated synthetic fertilizer levels in experimental plots ranging from 6.9% increase to 53.3% decrease in total N relative to control plots that received a standard amount of fertilizer. The effects on coffee yields, soil glomalin production by mycorrhizal fungi, and wasp diversity were examined. Yield and glomalin decreased, but parasitoid diversity increased with greater reductions in fertilizer application six months after application. Reducing fertilizer use may bolster biological control assemblages, while glomalin is more directly dependent on plant production.