During startup and commissioning of a modified Ludzack-Ettinger (MLE) membrane bioreactor (MBR), Pima County Wastewater Management Division (PCWMD) staff were concerned with the total nitrogen concentration (TN) in the plant effluent. Whereas in the traditional MLE process, increasing recycle ratio increases the TN removal, in this particular process increasing the recycle ratio proved to actually decrease TN removal. Influent five-day biochemical oxygen demand (BOD5) was also found to be only 50% of design. The process was found to be very sensitive to recycle ratio due to oxygen entering the anoxic zones. Increased process control testing provided insights into the process operation. Based on these data, significant changes were made to equipment operation to lower the aeration basin dissolved oxygen (DO) concentration. In addition, the recycle ratio was managed to minimize oxygen transfer to the anoxic zones. These operational changes improved TN removal beyond that predicted in the Biowin® model used for design. This paper describes the findings related to the operation of this MBR facility under abnormal conditions and some of the factors that were found to impact TN removal.