This is the first research to show that 3‐chloro‐1,2‐propanediol (3‐MCPD) was formed upon the action of 0.1% pancreatin at the early stage of soy sauce fermentation with Aspergillus oryzae and mixtures of soy flakes and wheat flour. A series of experiments were then performed to gain insight into such 3‐MCPD formation. Results showed that adding 0.1% pancreatin causes slightly decreased reducing sugar content but significantly increased 3‐MCPD, without significant changes in amino nitrogen, total nitrogen, and total acid contents. 3‐MCPD was formed by the action of different exogenous lipases (pancreatic phospholipase, Candida antarctica lipase B [CALB], and phospholipase A2). Further, soybean oil (not lecithin) could facilitate the 3‐MCPD formation upon the action of CALB, phospholipase A2, and pancreatic lipase due to the substrate specificity. Without adding such enzymes, all soy sauce koji with soybean oil had detectable 3‐MCPD, indicating that lipase may bind to the substrate via covalent bonding and chloride ions exert nucleophilic attack to form 3‐MCPD esters (which were hydrolyzed to release 3‐MCPD). Further studies are required to clarify precise mechanisms underlying the 3‐MCPD formation in the presence of exogenous lipase especially phospholipases. PRACTICAL APPLICATIONS: To avoid the prevalence of 3‐MCPD brewing in soy sauce, this manuscript gives the theoretical basis.