Microbial production of 1,3-propanediol (1,3-PD) has attracted the interest of scientists for decades. Its product offers an environmentally friendly and sustainable alternative to fossil-based raw materials for chemical synthesis. Citrobacter freundii is one of the natural producers of 1,3-PD known for its ability to yield it in significant titers. An efficient bioprocess requires an in-depth understanding of the factors that influence the performance of its biocatalyst. The effects of pH, temperature, stirring rate, and substrate concentration on glycerol fermentation in fed-batch cultures of C. freundii AD119 were investigated in this study. In addition to monitoring the kinetics of substrate utilization and the formation of the final products, the concentration of 3-hydroxypropionaldehyde (3-HPA), an inhibitory intermediate of glycerol bioconversion, was analyzed. When the optimal working conditions were used (pH 7.0, temperature 30 °C, stirring rate of 80 rpm, and glycerol concentration below 15 g/L during the fed-batch phase), 53.44 g/L of 1,3-PD were obtained. When the process was performed at temperatures of 33 °C or higher or in acidic pH (6.5), an elevated concentration of 3-HPA was observed and the process halted prematurely.