Oil palm-based agroforestry systems (AFS) can promote soil organic carbon (SOC) sequestration, but the links among plant richness, microbial communities, and SOC persistence remain only partially understood. Here, using long-term AFS plots and oil palm (Elaeis guineensis) monocultures in the Amazon, we show that AFS enhances microbial activity and assembles distinct microbial communities, while selects for contrasting microbial life strategies associated with resource acquisition and growth. These changes are accompanied by increases in particulate (POM-C; up to ∼300% and assumed as more labile) and mineral-associated (MAOM-C; up to ∼200% and assumed to be more persistent) SOC, with effects primarily dependent on plant species composition. Microbial necromass carbon (MNC) accumulation in AFS demonstrated similar increase and it was dominated by fungal necromass (∼64%) vs. bacterial necromass (∼36%). However, the contribution of MNC to SOC was decoupled from increases in MNC contents, accounting for a maximum of ∼27% of the bulk SOC in AFS (while ∼25% in monoculture), challenging the prevailing paradigm that multi-species plant cultivation and high microbial activity are major drivers of MNC contributions to SOC. These findings highlight ecosystem-level interactions as determinants of SOC sequestration and offer the first insights into MNC accumulation pathways in Amazonian agricultural systems.