Reducing nitrogen pollution across the food chain requires the use of clear and comprehensive indicators to track and manage losses. The challenge is to derive an easy-to-use robust nitrogen use efficiency (NUE) indicator for entire food systems to help support policy development, monitor progress and inform consumers. Based on a comparison of four approaches to NUE (life cycle analysis, nitrogen footprint, nitrogen budget, and environmental impact assessment), we propose an indicator for broader application at the national scale: The whole food chain (NUEFC), which is defined as the ratio of the protein (expressed as nitrogen) available for human consumption to the (newly fixed and imported) nitrogen input to the food system. The NUEFC was calculated for a set of European countries between 1980 and 2011. A large variation in NUEFC was observed within countries in Europe, ranging from 10% in Ireland to 40% in Italy in 2008. The NUEFC can be used to identify factors that influence it (e.g., the share of biological nitrogen fixation (BNF) in new nitrogen, the imported and exported products and the consumption), which can be used to propose potential improvements on the national scale.