Knowledge of the mathematical models of the fermentation processes is indispensable for their simulation and optimization and for the design and synthesis of the applicable control systems. The paper focuses on determining a dynamic mathematical model of the milk fermentation process taking place in a batch bioreactor. Models in the literature describe milk fermentation in batch bioreactors as an autonomous system. They do not enable the analysis of the effect of temperature changes on the metabolism during fermentation. In the presented extensive multidisciplinary study, we have developed a new mathematical model that considers the impact of temperature changes on the dynamics of the CO2 produced during fermentation in the batch bioreactor. Based on laboratory tests and theoretical analysis, the appropriate structure of the temperature-considered dynamic model was first determined. Next, the model parameters of the fermentation process in the laboratory bioreactor were identified by means of particle swarm optimization. Finally, the experiments with the laboratory batch bioreactor were compared with the simulations to verify the derived mathematical model. The developed model proved to be very suitable for simulations, and, above all, it enables the design and synthesis of a control system for batch bioreactors.