Objective This study aimed to evaluate the current status of cleaning and disinfection management for digestive endoscopy, provide data for standardization processing techniques, and improve the quality of cleaning and disinfection. Methods Two reviewers independently and comprehensively searched the PubMed, Cochrane Library, EMBASE, Web of Science, CNKI, Wanfang, and CBM databases on February 1, 2023. The inclusion and exclusion criteria were strictly followed during the literature survey and data extraction. All observational studies detailing the current cleaning and disinfection management status for digestive endoscopy in hospitals were included. Meta-analysis was performed using STATA 16.0 software. Results After removing different articles, the meta-analysis finally included 54 articles associated with multiple countries. The authors favor auditing staffers to confirm compliance with guidelines. The meta-analysis results indicated a configuration rate of 76% (95% CI: 68–83%) for separate rooms designated for reprocessing; 79% (95% CI: 72–84%) for reprocessing rooms with adequate ventilation; 30% (95% CI: 24–36%) for automated endoscope washer-disinfectors; 68% (95% CI: 55–81%) for complete protective equipment usage; 90% (95% CI: 83–95%) for the configuration rate of endoscope and accessory storage cabinets; 50% (95% CI: 38–61%) for changing enzymatic-type detergents after each use; 51% (95% CI: 30–71%) for the use of purified or sterilized water for final rinsing; 80% (95% CI: 70–88%) for monitoring disinfectant concentration; 87% (95% CI: 80–93%) for microbial monitoring; and 44% (95% CI: 26–62%) for the usage of protective equipment. Conclusion The configuration of the automated endoscope washer-disinfector, non-standard cleaning and disinfection procedures, and a lack of occupational protection awareness among personnel responsible for cleaning and disinfecting digestive endoscopy were all apparent issues. It was suggested that all departments enhance their levels of management and supervision, standardize reprocessing procedures and quality control details, upgrade hardware facilities and spatial layouts, reinforce personnel training, and increase staff awareness of nosocomial infection risks.