This work presents a comparative study between two different methods for the preparation of mediator-modified screen-printed electrodes, to be used as detectors in a reliable flow injection system for the determination of the nicotinamide adenine dinucleotide (NADH) coenzyme. The best strategy was selected for the final development of compact biosensors based on dehydrogenase enzymes. For the first immobilisation strategy, different redox mediators were electropolymerised onto the SPE surface. The second immobilisation strategy was carried out using polysulfone–graphite composites, which were deposited by screen-printing technology onto the screen-printed electrode (SPE) surface. Both methods achieved an effective and reliable incorporation of redox mediators to the SPE configuration. Finally, a flow system for ammonium determination was developed using a glutamate dehydrogenase (GlDH)-Meldola’s Blue (MB)-polysulfone-composite film-based biosensor. The stability of the redox mediators inside the composite films as well as the negligible fouling effect observed on the electrode surface improve the repeatability and reproducibility of the sensors, important features for continuous analysis in flow systems. Furthermore, the optimised bio/sensors, incorporated in a flow injection system, showed good sensitivities and short response times. Such a good analytical performance together with the simple and fast sensor construction are interesting characteristics to consider the polysulfone-composite films as attractive electrochemical transducer materials for the development of new dehydrogenase-based SPEs.