In order to adapt to the market trends that are moving towards ready-to-use products cod fish industry is including into their industrial operations as the desalting step. The desalting process is a high cost and time demanding operation. The optimization of the desalting process is of vital importance for the fish industry in order to assure the homogeneity and predictable concentration of sodium chloride in the final hydrated cod fish product. On the other hand, consumers are more aware about the necessity to bring sodium consumption down to healthy levels to prevent cardiovascular diseases. The application of rapid and simple analytical methodologies that permit the control of the process and ensure food quality is essential in the food industries. This work reports the optimization and application of two analytical methodologies with the objective of monitoring the variation of sodium chloride concentration during cod desalting process. A flow injection analysis system was developed based on the reaction between chloride and silver nitrate, and the formed precipitate was assessed spectrophotometrically as a turbidity change. A Fourier-mid infrared spectroscopy attenuated total reflection method was also applied. Different chemical and physical parameters of the flow injection system were studied and the analytical characteristics of both systems were compared.