The leakage of genetically engineered microorganism (GEM) at the beginning of operation was the important content for ecological risk assessment when GEM was inoculated in a membrane bioreactor (MBR) for bioaugmentation. The effects of different operating conditions on leaking density and intercepting efficiency of GEM were investigated in a submerged microfiltration MBR at the beginning of operation. The interception characteristics were also discussed. The results showed that different operating conditions had different influences on intercepting efficiency: higher sludge concentration was profit for interception, while higher aeration intensity and flux had opposite effects on interception. When the inoculated density of GEM was 1.0×1010 CFU/mL, the leaking densities varied from 1.0×102 CFU/mL to 2.5×102 CFU/mL under different operating conditions at the beginning of operation and the maximum intercepting efficiency could be higher than 8 lg. The main factors determining intercepting efficiency at the beginning of operation were membrane module interception, sludge adsorption as well as suspended GEM transfer inhibition and their contribution shares under certain conditions were 82.3%, 14.9% and 2.8%, respectively. Gel layer formation during MBR stable operation was helpful to increase intercepting efficiency. The contribution shares for GEM interception of membrane module, sludge and gel layer were 75.3%, 10.7% and 14.0%, respectively, under certain conditions.