Soil quality assessment is essential due to increasing demands for evaluation of conservation practices and environmental services in agroecosystems. This need is also recognized in the USDA-NRCS Conservation Effects Assessment Project (CEAP). Based on extant soil quality assessment tools, including the Soil Management Assessment Framework (SMAF), a new soil quality and ecosystem function assessment tool was established by integrating site-specific factors, ecosystem functions, and management associated with soil quality. The Natural Resources Inventory dataset and outputs of EPIC-APEX model simulations were applied in this study. Soil quality indicators corresponding to different ecosystem functions were screened and interpreted to calculate scores, modified by site-specific factors. An artificial neural network model was developed to bridge soil quality, soil ecosystem functions and management. The soil quality and ecosystem function assessment tool will be applied to conservation practices and environmental evaluation in agro-ecosystems.