Objectives To reduce the unpleasant odor during 1-deoxynojirimycin (DNJ) production, the genes of leucine dehydrogenase (bcd) and phosphate butryltransferase (ptb) were deleted from Bacillus amyloliquefaciens HZ-12, and the concentrations of branched-chain short fatty acids (BCFAs) and DNJ were compared. Results By knockout of the ptb gene, 1.01 g BCFAs kg(-1) was produced from fermented soybean by HZ-12 Delta ptb. This was a 56% decrease compared with that of HZ-12 (2.27 g BCFAs kg(-1)). Moreover, no significant difference was found in the DNJ concentration (0.7 g kg(-1)). After further deletion of the bcd gene from HZ-12 Delta ptb, no BCFAs was detected in fermented soybeans with HZ-12 Delta ptb Delta bcd, while the DNJ yield decreased by 26% compared with HZ-12. Conclusions HZ-12 Delta ptb had decreased BCFAs formation but also maintained the stable DNJ yield, which contributed to producing DNJ-rich products with decreased unpleasant smell.