Soil microbial communities play a crucial role in the accumulation and stabilization of soil organic carbon (SOC) through complex processes involving plant residue transformation and mineral interactions. These processes are influenced by plant inputs and modulated by soil properties that are mostly determined by the parent material. However, our understanding is limited regarding the manner in which vegetation and parent material affect microbial community structure, necromass accumulation, and their subsequent impact on SOC storage. To bridge this knowledge gap, we conducted an in-depth investigation focusing on the top-down influence of vegetation type and the bottom-up effect of parent material on microbial-mediated carbon transformation across soil profiles in a tropical region. Our study encompassed 42 sites on three parent materials (basalt, granite, and marine sediments) and four vegetation types (rubber, banana, areca plantations and uncultivated grassland). Soil samples were collected at 0–20, 20–40, 40–80, and 80–100 cm depth. Microbial community structure and necromass were quantified using microbial biomarkers of phospholipid fatty acids and amino sugars, respectively. In rubber plantations, we observed a trend toward higher microbial biomass that, though not significant when compared to other vegetation types, transformed to a significantly higher accumulation of microbial necromass. This increase in microbial necromass was linked to the accumulation of SOC facilitated by the presence of clay size minerals in clayey soils developed from basalt. In particular, basaltic soils were dominated by bacteria, which facilitated the accumulation of bacterial necromass that significantly bolstered its contribution to SOC. In contrast, in sandier soils developed from granite and marine sediments, fungal communities and necromass dominated due to the propensity of fungi for coarser soil environments. Overall, the main impact of vegetation on microbial communities and necromass accumulation was primarily demonstrated for the topsoil. Differences in soil texture arising from different parent materials exert significant effects on the fungal-to bacterial-biomass and necromass ratios, consequently influencing the contribution of fungal and bacterial necromass carbon to SOC across soil profiles. Our study underscores the pivotal role of parent material in governing tropical profile-scale soil carbon storage by shaping the structure of microbial communities and influencing the retention of microbial necromass.