Background: We integrated a standardized questionnaire focusing on adverse events and performance measures in gastrointestinal endoscopy as a mandatory component of the electronical medical record. Methods: This retrospective study was conducted using prospectively collected data on quality parameters and adverse events (AEPM) for all diagnostic and therapeutic endoscopic procedures at our center between 2018 and 2020. Results: A total of 7532 consecutive endoscopic procedures were performed in 5035 patients. The proportion of high-risk examinations and high-risk patients was 20% and 23%, respectively. Severe adverse events (AEs, n = 21) occurred in 0.3% of procedures and significantly more often in patients with an ASA score > II (0.6%, p < 0.01). We observed no long-term morbidity after severe AEs. Mortality was 0.03% (n = 2). Following screening colonoscopy (n = 242), four endoscopists documented AEPM in more than 98% of the examinations. The cecal intubation rate was 97%, and the mean adenoma detection rate 60%. The quality of lavage was documented in 97% (rated as good in 70% and moderate in 24%). Conclusions: The risk of adverse events is significantly increased in patients with an ASA score > II, which should be considered when choosing treatment methods and precautionary measures. Continuous recording of AEPM can be effectively integrated into the clinical reporting process, enabling analysis of the data and feedback to be provided to endoscopists.