Soils are now recognized as key components in the design of sustainable agricultural practices within the agroecological framework. They are the place of many ecological functions achieved by living organisms interacting with each other and which support the sustainable provision of agrosystem services. In the context of the transformation of agriculture and to improve the sustainability and resilience of family farming, it becomes urgent to promote soil ecological functions, to intensify them by appropriate practices considering the socioeconomic constraints, and finally, to be able to monitor them. Here, to improve our consideration of the soil functions for a sustainable agriculture, we first rely on the ecological theories of terrestrial ecosystem functioning to better establish the concept of sustainable functions in agroecosystems. We then propose a methodological framework, called SECURE (for "Soil Ecology Cure"), that aims to optimize the ecological functions of the soil for a sustainable supply of ecosystem services. This framework relies on the involvement of stakeholders and is illustrated by a case study in Madagascar where the different steps of the SECURE approach have been applied.