Biofilm contributes significantly to bacterial persistence in endoscope channels. Enhanced cleaning methods capable of removing biofilm from all endoscope channels are required to decrease infection risk to patients. This head-to-head study compared cyclic build-up biofilm removal of an automated endoscope channel cleaner (AECC) to standard manual cleaning according to instructions for use (IFU) in polytetrafluorethylene channels. The automated cleaner significantly outperformed manual cleaning for all markers assessed (protein, total organic carbon, viable bacteria) in 1.4 mm and 3.7 mm channels representing air/water/auxiliary and suction/biopsy channels respectively. Manual cleaning failed to remove biofilm from the air/water and auxiliary channels. According to the IFU, these channels are not brushed, suggesting a potential root cause for a portion of the numerous endoscopy associated infections reported in the literature. AECC shows potential to deliver enhanced cleaning over current practice to all endoscope channels and may thereby address infection risk.