The challenging disinfection process for the elevator mechanism on duodenoscopes and linear echoendoscopes has been identified as a source of clinically significant bacterial transmission. Despite increased awareness, there continues to be a lack of definitive guidelines for bacterial culturing protocols for elevator-containing endoscopes. To compare two different prospective bacterial surveillance protocols for duodenoscopes and linear echoendoscopes with regard to accuracy, efficiency, and cost. Consecutive duodenoscopes and linear echoendoscopes used at a single tertiary care center were reprocessed following hospital and manufacturer guidelines, dried using an automatic endoscope-drying machine, and hung overnight in an upright position. Following reprocessing, culture samples were sequentially obtained from each endoscope using two methods, first, the brush protocol followed immediately by the swab protocol. A total of 532 primary cultures were collected from 17 duodenoscopes and eight linear echoendoscopes. Of these, 266 cultures gathered using the brush protocol were negative, while 266 cultures gathered using the swab protocol resulted in three positive cultures (1.1%). Positive cultures showed Enterobacter cloacae and Klebsiella pneumoniae from one duodenoscope and two linear echoendoscopes. Yearly, the brush protocol amounts to approximately 520 nursing hours, and the swab protocol takes an estimated 42 nursing hours. Annually, the swab protocol could save over $26,500 and 478 nursing hours. The proposed swab protocol was superior to the brush protocol when evaluating the presence of residual bacteria on elevator-containing endoscopes following reprocessing and saves cost and nursing hours. © 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.