In a context of global soil biodiversity loss, we need to find effective way to measure the functions supported by biodiversity. This constitutes the main challenge of soil health assessments, particularly in the agroecological transition context. The most shared definition of soil health is based on the ability of soil to function (Karlen et al., 1997) and to provide ecosystem services. However, most methods focus on stock measurements rather than functions. Also, measurements are usually performed in the laboratory, reflecting the potential level of soil functions rather than true field performance. To overcome these methodological limitations, a new framework is proposed to assess soil health based on functional methods that considers the links between abiotic and biotic soil compartments. This method, called Biofunctool®, incorporates nine rapid, cost-effective, and in-field indicators to evaluate three main soil functions: C transformation, nutrient cycling, structure maintenance. The capacity of the set of indicators to assess the impact of land management on soil health will be illustrated in various agroecological contexts in the tropics. Biofunctool® allows to better understand the impacts of agricultural practices on soil functions driven by soil biodiversity and could be in the future included in environmental analyses.