The transformation of the food and industrial agricultural production system into adaptative and sustainable systems capable of being productive within social, environmental, and economic limits is a crucial factor in reducing the risk to food security and to economic growth. However, the analysis structure of the effect of these variables in sustainable environments remains unknown, whereby the technology and processes are considered as variables of the equivalent critical level as those already described. The purpose of this study is to design a model that enables the characterisation of the agri-food sector based on the determination of sustainable variables from a sustainable and integral systemic approach. Tools, such as the viable system model, are employed to analyse the dynamics and generate the balanced scorecard, to which the items of learning and continuous improvement are added. Lastly, the impact of the principles of sustainability versus the variation of sustainability in the agri-food system is revealed, which is useful in determining the appropriate levels to guarantee a balance in the foundations of circularity. From a systemic approach, this model can be adopted by agronomists and scientists to design alternative strategies for the management of food sustainability.