With the development of agroecology, soil plays a particularly important role in the design of sustainable agricultural practices. The soils are the place of many processes operated by living organisms interacting with one another. Soil biodiversity performs various processes which determine the main aggregated functions and finally agrosystem services and sustainability. The understanding of these relationships is particularly important in a global context where biodiversity, including the soil one, is highly threatened. It becomes urgent to promote these ecological processes, to intensify them by appropriate practices considering the socio-economic constraints, and finally, to be able to measure them. Revisiting the ecological theories of the terrestrial ecosystem functioning is a need to improve our consideration of the soil in the agroecological transition. This theoretical approach is illustrated by four studies conducted in the tropics demonstrating the possibility to intensify the soil ecological processes and to solve agronomic dysfunctions. Finally, we highlight the need to define soil indicators based on ecological processes for an appropriate measurement of this intensification and we propose a methodological framework to optimize soil ecological functions for a sustainable supply of agrosystem services.