In the Central Valley of Costa Rica at Finca la Hilda, a Rainforest Alliance Certified coffee farm owned by the Doka Estate Coffee Company, we investigated the soil chemical properties and microbial community composition associated with four native shade tree species in a coffee agroforestry system. The tree species included in this study were Anona muricata L., Diphysia Americana Mill., Persea Americana Mill., and Quercus spp.L. Plots measured 20 by 30 meters and were replicated three times for each shade tree species except for Quercus spp., which only had two replications.  A three factorial arrangement in a split-split plot design was chosen to study the effects of tree species, sun or shade position, and whether EM© affected soil chemical properties. 12 composite soil samples were collected from each plot in 2008, after which time we applied EM© as recommended by the manufacturer.  Soil samples were collected a second time, in 2009. In this two-year study, we collaborated with the Center for Tropical Agriculture and Education (CATIE) and EARTH University, both located in Costa Rica. The results of this study indicate that the species of native tree has a statistically significant effect on soil ammonium, nitrate, total dissolved nitrogen, and magnesium. Sun or shade position has a significant effect on dissolved organic nitrogen dissolved organic carbon. A causal relationship for these effects, however, could not be established.  We also found that the species of native tree is significantly correlated to the abundance of soil fungi. Finally, Effective Microorganisms© in combination with the tree species and sun or shade position had a significant interaction effect on soil ammonium.  A comparison of coffee yield data among the different plots would shed light on which of the four tree species are associated with higher coffee yields.