In recent decades, mounting evidence has indicated that the expansion of oil palm (OP) plantations at the expense of tropical forest has had a far pernicious effect on ecosystem aspects. While various deforestation-free strategies have been proposed to enhance OP sustainability, field-based evidence still need to be consolidated, in particular with respect to savanna regions where OP expansion has recently occurred and that present large area with potential for OP cultivation. Here we show that the common management practice creating within the plantation the so-called management zones explained nearly five times more variability of soil biogeochemical properties than the savanna land-use change per se. We also found that clayey-soil savanna conversion into OP increased total ecosystem C stocks by 40 ± 13 Mg C ha−1 during a full OP cultivation cycle, which was due to the higher OP-derived C accumulated in the biomass and in the soil as compared to the loss of savanna-derived C. In addition, application of organic residues in specific management zones enhanced the accumulation of soil organic carbon by up to 1.9 Mg ha−1 year−1 over the full cycle. Within plantation, zones subjected to organic amendments sustained similar soil microbial activity as in neighboring savannas. Our findings represent an empirical proof-of-concept that the conversion of non-forested land in parallel with organic matter-oriented management strategies can enhance OP agroecosystems C sink capacity while promoting microbe-mediated soil functioning. Nonetheless, savannas are unique and threatened ecosystems that support a vast biodiversity. Therefore, we suggest to give priority attention to conservation of natural savannas and direct more research toward the impacts of the conversion and subsequent management of degraded savannas.