The need for a more sustainable agri-food system is a topic that has attracted growing interest in recent years. Several international and European policies such as Agenda 2030 and the European Green Deal have been defined with the aim of making agri-food systems more sustainable at all stages of the supply chain, from production to consumption. Particularly, the European Union concentrates several policies on it. Therefore, the assessment of the level of sustainability among the states of the European Union is a key aspect to properly address and evaluate the implementation of these policies. The objective of this paper is to measure the sustainability of the global agri-food supply chain (AFSC) of the European Union countries through the application of a multi-criteria analysis. In particular, the method used is the Multiple Reference Point Partially Compensatory Indicator, which allows the creation of composite indicators using different levels of compensation across them. A set of 50 indicators, referred to 2011 and 2019, were built and then divided into the three basic dimensions of sustainability (economic, social and environmental), aggregated into the four main AFSC sectors (agriculture, food industry, distribution, and consumption) in order to obtain an overall sustainability index. Through such an index we provided a sustainability ranking for the EU countries, while the analysis of dimensions of each sector contributed to increase the knowledge about the supply chain that can be used by decision-makers. According to the results, Italy achieved the best level of sustainability of the AFSC with a value of 48.53, followed by Sweden, Austria, Spain, France, Germany, the Czech Republic, Portugal and Slovakia. In relation to the different sectors, the biggest problems were observed in the consumption sector, where most countries did not perform well, especially for the social dimension (e.g. excess of overweight and obese persons). In contrast, the performance of the agricultural sector was good, with few exceptions, showing a fair state of sustainability.