Application of Quality by Design (QbD) approaches to food processes requires the development and identification of complex mathematical models. With reference to soy sauce desalting by electrodialysis (ED), the aim of this work was to combine several Process Analytical Tecnology (PAT) tools, such as Near Infrared spectroscopy (NIR), level and conductivity probes, and a control strategy of the electric current generator to increase the amount of information of single desalting experiments for ED modelling. Soy sauce volume and electric conductivity as well as the electric voltage and current applied to the ED stack were precisely measured at high sampling rates. NIR models of the main soy sauce physicochemical properties (density, osmotic pressure, electric conductivity; salt and non-salt solid concentrations), needed for ED modelling, were developed and applied to several experiments resulting in good predictions. The results indicate that the demonstrated procedure enhances ED process characterization for desalting of soy sauce or other food systems.