Soil carbon cycling is a complex process that has the potential to tremendously impact the future course of global climate change. It is unknown whether soil will serve as a net carbon source, thereby amplifying global warming, or if soil will act as a carbon sink, thus negating the effects of increasing atmospheric carbon dioxide. The missing link in this controversy may be found in the dynamics of carbon turnover in deeper soil. Up to 70% of the carbon stored in soils is found at depths greater than 20 cm. Therefore, understanding soil carbon turnover at different depths within the profile is critical in predicting the response of ecosystems to global climate change. This study investigated the potential mechanisms involved in the turnover of deep soil carbon and compared these findings to surface processes. We explored the links between microbial community composition and soil characteristics throughout the soil profile (up to 1.2 meters) at Mount Kinabalu, Borneo on two different geologic substrates, serpentine and meta-sedimentary rock. As expected, microbial abundance and activity was found to be highest in the upper portion of the soil profile. Interestingly, the lowest enzyme activity was found in the 50-75 cm depth interval rather than deeper, which may indicate there is higher microbiological activity deeper in the profile than previously suspected. The soil profile below 15 cm showed significantly reduced biomass of all lipids analyzed. Surprisingly, the different parent materials did not differ in their microbial community structure and function, except for a significantly higher fungal biomass present on the ultrabasic substrate. Results are anticipated to provide valuable information pertinent to global change modeling efforts and improve predictions of global climate change by clarifying the relationships between soil microorganisms and soil characteristics at increasing soil depths.