This chapter first discusses the potential of trees to modify the soil and its impact on soil biota. The exploration of the linkages between the biological activity of soil organisms in agroforestry systems and their impact on soil-based ecosystem services and soil health follows next. Then recent advances in soil health monitoring systems and approaches to harnessing the complementary nature of local and scientific knowledge are discussed. We conclude by highlighting the role of agroforestry practices in adaptive and multifunctional land management with a view to enhancing soil health and agricultural sustainability, as well as recommendations for future research.