The rapid growth of the livestock sector has altered the way the sector influences global nutrient flows and emissions, with repercussions on environmental and public health issues. Designing interventions for better environmental sustainability will require a framework and indicators adapted to the increasingly long, and complex livestock supply chains. To develop such a framework, we reviewed existing studies and found that four methods were used previously to analyse nutrient use in the livestock sector, namely a nutrient balance, nutrient use efficiency (NUE), material flow analysis and life cycle assessment. Among these methods, NUE appeared as a suitable approach to benchmark nutrient management that can be integrated in life cycle approach to compute the supply chain level NUE, which is proposed as a valuable indicator of nutrient management sustainability. To this end, we developed a comprehensive framework of indicators to assess the sustainability of nutrient use. The framework encompassed three indicators, including the life-cycle nutrient use efficiency (life-cycle-NUE), life-cycle net nutrient balance (life-cycle-NNB) and nutrient hotspot index (NHI). It was tested and the indicators proposed were found to be suitable to describe nitrogen (N) and phosphorus dynamics and were all needed. This framework requires detailed data, which are highly variable at global level, resulting in large uncertainties of the results. Focusing on N, we proposed a method, which relies on a global sensitivity, to identify the important inputs parameters that contribute significantly to the variance of the results, using the Global Environmental Assessment Model (GLEAM) dataset. The results showed that uncertainties of a few important input parameters, such as manure deposited and applied could explain most of the variance of N use indicators. Fixing non-important parameters and substituting important parameters in GLEAM for new field survey data, improved the results of N use indicators. Subsequently, we applied the framework to assess N use, flows and emissions, in the global pork supply chains and to evaluate the effects of feeding swill to pigs as a strategy to integrate better livestock in a circular bio-economy. The results showed that N emissions into the environment amount to around 14.7 Tg N y −1 , of which 68% is lost to watercourses. These results showed that the efficiency of N use and the magnitude of N losses per unit of area depend chiefly on the region, origin of feed, and manure management. The substitution of swill for grains and soybeans resulted in the improvement of N use indicators and abate N emissions. Implementing swill feeding would require innovative policies to guide the collection, treatment, and usage of swill, and ensure safety and traceability. Applying the framework to global livestock supply chains showed that they are responsible for around one-third of human-induced N emissions (65 Tg N y −1) of which 63% take place in 2 regions (i.e. South Asia and East and Southeast Asia), and 61% at t...