The fermentative production of 1,3-propanediol (1,3-PDO) by Klebsiella pneumoniae under different initial substrate concentrations (between 5 and 110 g/L) was investigated. It was found that glycerol was almost 100% utilized and 1,3-PDO production increased up to 20 g/L of influent substrate concentration, but there was a significant decrease in both glycerol consumption and 1,3-PDO production at substrate concentrations exceeding 20 g/L. Furthermore, pH control was essential, and a lack of pH control negatively effects of 1,3-PDO production. In the second part of the study, two microorganisms, namely Clostridium beijerinckii NRRL B593 and K. pneumoniae were comparatively studied in terms of their 1,3-PDO productivity under pH controlled conditions. Higher 1,3-PDO production was achieved under pH controlled fermentation conditions (pH = 7) for both microorganisms. Even though the two microorganisms had almost the same 1,3-PDO yield (0.60 mol/mol for C. beijerinckii, 0.61 mol/mol for K. pneumoniae) at the end of fermentation period, K. pneumoniae completed the 1,3-PDO production in one-third of the time (t = 8 h with a productivity of 1.34 g/L/h) than C. beijerinckii (t = 24 h). The results of this study clearly indicated that a substrate inhibition is a challenge that needs to be studied further for higher productivities.