The reliance on inorganic fertilizers, along with the simplification of cropping systems and agricultural landscapes, fueled tremendous increases in yield while generating severe consequences for the biosphere, human health, and biodiversity. There is a critical need to address these issues and transition to a more sustainable approach to soil management and food production. Ecosystem ecology provides a flexible systems approach for understanding the complex and dynamic interactions among organisms, their environment, and agricultural management, which ultimately govern biogeochemical cycling and soil-mediated ecosystem services. This chapter reviews concepts from ecosystem ecology and related disciplines that form the foundation of ecological nutrient management (ENM), including how communities of plants and soil organisms govern soil organic matter dynamics and nutrient cycling. It presents the foundational principles of ENM and discuss key management practices that extend these principles into desirable improvements in agroecosystems, emphasizing how ecosystem science can be leveraged to implement ENM effectively.