Due to the continuous growth of soap, detergent, and biodiesel industries, glycerol production as a byproduct has increased substantially, resulting in a significant reduction of its price. Glycerol can be fermented with many bacterial strains to produce several valuable chemicals like 1,3-propanediol (1,3-PD). This organic compound is highly versatile, useful for producing a wide range of polymers such as polyesters, polyester, polyurethane, and trimethylene terephthalate; hence, the industrial production of 1,3-PD is highly appealing. The fed-batch cultivation of Clostridium butyricum, using glycerol as substrate, was simulated using Matlab-Simulink and an Orthogonal Collocations on Finite Elements procedure (OCFE) was implemented, using AMPL software, to find the optimal path of substrate concentration in the reactor that could maximize the production of 1,3-PD. Then a Model Predictive Control (MPC) was applied to follow the optimal setpoints, given by AMPL, of substrate concentration and temperature reactor. Finally, the performance achieved in 40 hours of simulation, with a final concentration and productivity of 74.94 g/L and 1.874 g/L/h respectively, gave similar results of 1,3-PD production by other microorganisms like C. diolis and K. pneumoniae.