In this chapter we propose a conceptual framework to guide understanding of the complex nature of the underlying biological processes involved in soil organic carbon (SOC) sequestration. We analyze, step by step, the conditions that promote an accumulation of organic matter in the soil and the maintenance of large SOC stocks. We will focus on the process of soil aggregation, which allows the local creation of conditions unfavorable to microbial activity or disconnection among decomposers and their organic resources, thus contributing to the temporary storage of SOC at different levels of decomposition and different depths in soils. Taking the earthworm drilosphere as an example, we consider the biotic and abiotic factors in their genesis, their diversity and conditions for the stabilization or disaggregation of these structures. We finally discuss the theoretical and technical bottlenecks that impede research providing a clearer understanding, needed to design better management practices that would enhance carbon sequestration in natural and managed ecosystems.