Nutrients, such as Nitrogen (N) and Phosphorus (P), are critical for net primary productivity in agricultural and non-agricultural ecosystems and are consequently important for food and climate security. However, rising nutrient inputs to agricultural production and the biosphere have led to severe environmental issues. Quantifying nutrient budgets, including the nutrient inputs and outputs of a defined system or within a spatial boundary, is an essential step towards sustainable nutrient management, and also provides critical inputs to agronomic, biogeochemical, and climate models. Therefore, this session calls for research efforts on quantifying, analyzing, and/or projecting nutrient budgets on various system levels (e.g., crop and livestock production systems, integrated agro-food systems) and spatial scales (e.g., farms, watersheds, nations). This session aims to provide an opportunity to assess the advances and challenges in the existing nutrient budgeting methods and databases, and to engage discussions towards better quantification of nutrient budgets for various applications.