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Logging and forest conversion are occurring at alarming rates in the tropical forests of Southeast Asia. These disturbances alter soil chemistry, microbial diversity, and disrupt carbon cycling through shifts in litter decomposition. Direct links between microbial diversity and soil properties such as pH are well established; however, the indirect impacts of logging and forest conversion on microbial diversity and litter decomposition are poorly understood. We used surface (5 cm) soil to assess soil physicochemical properties, next-generation DNA sequencing to assess soil microbial diversity, and standardized litterbags to assess litter decomposition stabilization at five sites along a land use disturbance gradient in the tropical montane forests of Sabah state in eastern Malaysia. We used a hierarchical approach to explore how land use disturbance affects soil properties; how those soil properties in conjunction with land use disturbance affect soil microbial diversity; and how each of those factors affects litter decomposition and stabilization. We show that soil pH, total nitrogen, and bacterial diversity increase with time since disturbance; and sulfur, total carbon, percent sand, soil organic matter, and fungal diversity display a peaked response with peak around 100 years since the last disturbance. Fungal diversity is positively correlated with onsite forest cover, litter decomposition rate, and litter stabilization. Bacterial diversity shows a positive linear relationship with litter decomposition rates, but a peaked relationship with litter stabilization with peak around the mid-range of bacterial diversity. In summary, soils of the older forests harbor significantly greater microbial diversity and stabilize greater amounts of litter than soils of the younger forests and converted sites. Our results suggest that logging and forest conversion significantly affect soil microbial diversity and have lasting effects on carbon cycling in tropical montane forests.