The food processing value chain is facing numerous challenges on a multitude of levels. Furthermore, with the Food and Beverage industry being one of the biggest contributor to the economic sector within the European Union it is of great importance to optimise handling and processes along the value chain and processing technologies in the most sustainable and resilient manner. The process settings currently implemented fail to consider the process-product relationship leading to severe quality losses and unnecessarily high resource demands. Commonly implemented optimisation such as the black box approach lack the consideration of process induced dynamic changes within the product, thus, hindering a holistic process optimisation. To achieve this, a new systematic approach is required that encompasses product based hybrid models, data processing and measurement and control system that form the foundation for the development of digital twins of the product, the natural and technological environment. These digital twins apply physics based modelling in combination with data-driven methods to contextualize real-time measurements in such a way that dynamics of product quality can be understood, thus used for decision making in process control and finally allow for systematic optimisation of food processes.