This study investigates the application of crude glycerol to the production of 1,3-propanediol by immobilized cells of Bacillus pumilus. This is a novel application of a naturally occurring producer obtained from a wastewater storage pond in Thailand. Crude glycerol was obtained through the methanolysis of palm oil, which was catalyzed using rice bran lipase. Ten components of the fermentation medium were screened using a Plackett-Burman design. The statistical significance of the results was determined using multiple linear regression with a backward elimination approach. The significance level was set to 5 % (p < 0.05). Only crude glycerol, (NH4)2SO4, MgSO4, and CaCl2 significantly affected 1,3-propanediol production by immobilized B. pumilus. Furthermore, preliminary screenings of environmental conditions used for 1,3-propanediol production were conducted using a Plackett-Burman design. The results showed that the temperature, time, and quantity of immobilized cells were factors that significantly affected 1,3-propanediol yield. Therefore, the quantities of crude glycerol, (NH4)2SO4, MgSO4, and CaCl2 and the temperature, time, and quantity of immobilized cells were optimized using response surface methodology based on a Box-Behnken design. The model predicted a maximum 1,3-propanediol yield of 45.68 g/L with the following conditions: 60 g/L crude glycerol, 5 g/L (NH4)2SO4, 0.55 g/L MgSO4, 0.05 g/L CaCl2, a fermentation duration of 101 h, and a temperature of 25 °C, with 250 g of immobilized cells. The validation trials confirmed a production level of 44.12 ± 1.81 g/L, indicating a 2.86-fold production increase relative to the control group. Overall, this study demonstrates the potential of using crude glycerol as a substrate to improve the yields of 1,3-propanediol produced by B. pumilus.