The agri-food supply-chain represents a complex System-of-System (SoS), because it crosses different other sectors and involves many different actors. The System Engineering (SE) approach helps to identify boundaries as a line of demarcation between the system itself and its greater context, including the operating environment, without neglecting any aspect. Model-Based System Engineering (MBSE) was used, due to its capacity to realise more readable and compact documentation than other models. It uses System Modeling Language (SysML) to construct a structure, the behaviours, the requirements and the constraints of the system. The modelling method developed to design and implement a model is based on one of the main purposes of the agri-food SoS: the need of tracking and tracing useful information to realize a traceable and sustainable system. Agri-food supply-chain SoS was analysed through an iterative procedure model – developed in Papyrus open-source – that has the system requirements as the centre. The requirement diagram is composed of: consumer requirements, business requirements, legislation requirements and environmental requirements. The typical structure of the requirement package in SysML has inherent the parent-child relationship and responds in an appropriate manner to the system traceability. Papyrus can directly validate the designed model, without complex simulations, especially in the case of a high level of abstraction, which would be missing some implementation parameters necessary for the simulation of the technical phase. This type of validation allowed to check better and faster what has been developed through project simulations. This work presents the main results of the SE approach applied to the agri-food supply-chain. It represents a starting point for the choice of the technical traceability solution.