Tropical forest soils contain large pools of carbon, most of which is stored as soil organic matter. In spite of its significant role in the global carbon cycle, the dynamics of tropical soil organic matter, including the soil microbial communities that produce, maintain and decompose it, are poorly understood. This dissertation investigates controls on the structure and biogeochemical functions of soil microbial communities and soil organic matter, using a combination of laboratory experiments and natural gradients present at the Luquillo Critical Zone Observatory. First, we investigate linkages between soil enzyme activities, nutrient availability and plant roots in surface mineral soils through a greenhouse pot experiment. Three subsequent studies "dig deeper", by investigating microbial community structures and functions (carbon, nitrogen and phosphorus cycling capacity) along the upper 1.4 meters of soil profiles. Finally, we use NMR spectroscopy to profile the chemical composition of soil organic matter across various depths, soil and forest types, coupled with additional thermal and chemical analyses to evaluate acid-treatment effects on soil organic matter composition. We find that dynamic microbial communities exist along the upper 1.4 meters of tropical soil profiles and that, on a per biomass basis, subsoil microbial communities have similar capacity to participate in carbon and nutrient mineralization as their surface counterparts. While microbial activity is strongly correlated to soil carbon concentrations and hence energy availability, soil organic matter chemistry appears to be driven by landscape scale factors as well as pit-scale factors. Because even small amounts of active soil carbon below the surface few centimeters of the soil profile could produce significant carbon fluxes over large spatial and temporal scales, models that aim to predict the future changes to the global carbon cycle should begin to consider the capacity for carbon cycling to occur throughout the deep critical zone.