With the advent of Industry 4.0, many new approaches towards process monitoring, benchmarking and traceability are becoming available, and these techniques have the potential to radically transform the agri-food sector. In particular, the chilled food supply chain (CFSC) contains a number of unique challenges by virtue of it being thought of as a temperature controlled supply chain. Therefore, once the key issues affecting the CFSC have been identified, algorithms can be proposed, which would allow realistic thresholds to be established for managing these problems on the micro, meso and macro scales. Hence, a study is required into factors affecting the CFSC within the scope of Industry 4.0. The study itself has been broken down into four main topics: identifying the key issues within the CFSC; implementing a philosophy of continuous improvement within the CFSC; identifying uncertainty within the CFSC; improving and measuring the performance of the supply chain. However, as a consequence of this study two further topics were added: a discussion of some of the issues surrounding information sharing between retailers and suppliers; some of the wider issues affecting food losses and wastage (FLW) on the micro, meso and macro scales. A hybrid algorithm is developed, which incorporates the analytic hierarchical process (AHP) for qualitative issues and data envelopment analysis (DEA) for quantitative issues. The hybrid algorithm itself is a development of the internal auditing algorithm proposed by Sueyoshi et al (2009), which in turn was developed following corporate scandals such as Tyco, Enron, and WorldCom, which have led to a decline in public trust. However, the advantage of the proposed solution is that all of the key issues within the CFSC identified can be managed from a single computer terminal, whilst the risk of food contamination such as the 2013 horsemeat scandal can be avoided via improved traceability.