Soil fauna represent a substantial portion of life in soils and play a critical role in providing ecosystem services and maintaining and enhancing soil quality. This chapter focuses on the potential of two key soil faunal ecosystem engineers—earthworms and enchytraeids—as soil health indicators in agroecosystems. Both groups are widely distributed and share similar functions in soils, albeit at different scales. We examine how environmental conditions, soil management practices, and interactions between these faunal groups impact their populations. Further, we review the various methods used to sample them and assess their activity. Earthworms and enchytraeids are only recently being seriously considered as biological indicators for soil quality. While it is clear that both faunal groups are sensitive to external factors such as land use, management and climate, we demonstrate that translating their functions into a practical, accessible indicator remains a challenge. We end with proposing key directions for future research.