•C. beijerinckii DSM 791 is a robust organism for 1,3-PDO production from glycerol.•Replacing yeast extract with corn steep liquor increased cell growth and productivity.•Stable, long-term 1,3-PDO production was obtained in repeated batch fermentations.•Cell was engineered to overexpress GDH and DHAK.•1,3-PDO productivity increased 26.8–37.5% with a greatly increased growth rate. 1,3-Propanediol (1,3-PDO) production from crude glycerol, a byproduct from biodiesel manufacturing, by Clostridium beijerinckii DSM 791 was studied with corn steep liquor as an inexpensive nitrogen source replacing yeast extract in the fermentation medium. A stable, long-term 1,3-PDO production from glycerol was demonstrated with cells immobilized in a fibrous bed bioreactor operated in a repeated batch mode, which partially circumvented the 1,3-PDO inhibition problem. The strain was then engineered to overexpress Escherichia coli gldA encoding glycerol dehydrogenase (GDH) and dhaKLM encoding dihydroxyacetone kinase (DHAK), which increased 1,3-PDO productivity by 26.8–37.5% compared to the wild type, because of greatly increased specific growth rate (0.25–0.40h−1 vs. 0.13–0.20h−1 for the wild type). The engineered strain gave a high 1,3-PDO titer (26.1g/L), yield (0.55g/g) and productivity (0.99g/L·h) in fed-batch fermentation. Overexpressing GDH and DHAK was thus effective in increasing 1,3-PDO production from glycerol.