Agroforestry is recognized to have the potential to guide the transition to a multifunctional agriculture that successfully addresses the challenge of optimizing crop productivity while maintaining the provision of multiple ecosystem services. The majority of ecosystem processes depend on the soil as the critical and dynamic regulatory center and soil organisms contribute to a wide range of ecosystem services that are essential to the sustainable function of natural and managed ecosystems. Recent evidence has shown that there is strong linkage between aboveground biodiversity (vegetation/crops) and belowground biodiversity (soil organisms). This finding supports the concept that the integration of trees in agriculture can have profound impacts on soil-mediated ecosystem services.  Our study of Tree-Soil interactions is housed within a Land Health Surveillance Framework that involves standardized measurement protocols over sentinel sites (10 x 10 km blocks of land), within which a spatially stratified, randomized ground sampling scheme is implemented. Tree and shrub density are measured and soil samples taken in 100-m² sub-plots, which are nested within 1000-m² plots, in turn nested within 1-km² diameter clusters. The position of the clusters within 2.5 × 2.5 km tiles is also randomized. Soil samples from each plot are characterized using infrared spectroscopy as a front-line tool for screening soil properties. The strategic combination of a whole soil biota sampling protocol, molecular biology tools, and spectroscopic techniques within spatially-explicit sampling frameworks allows the systematic study of tree/soil biota interactions influencing soil-mediated ecosystem services in agricultural landscapes of East and Southern Africa.  Land Health Surveillance can provide a practical, evidence-based approach for considering soil biodiversity and other land health indicators when planning and evaluating land management interventions