The safety and effectiveness of propofol in more complex endoscopic procedures, such as endoscopic retrograde cholangiopancreatography, remain unknown. Thus, we aimed to evaluate propofol sedation during endoscopic cholangiopancreatography, ultrasound-guided intervention, and gastroduodenal stenting and examine risk factors for excessive sedation. We retrospectively analyzed data from 870 patients who underwent endoscopic treatment with propofol sedation for biliary and pancreatic disease between October 2020 and September 2021. Sedation included propofol and fentanyl, with continuous monitoring of vital signs and the bispectral index. The assessed risk factors included age, complications, body mass index, treatment duration, and specialty. Distal bile duct treatment (n = 367), hilar bile duct treatment (n = 197), post-small-intestinal reconstruction treatment (n = 75), endoscopic ultrasound-guided intervention (n = 140), and gastrointestinal obstruction treatment (n = 91) were performed. The rates of excessive sedation, hypoxemia, and hypotension were 7.8%, 6.0%, and 1.8%, respectively. Post-small-intestinal reconstruction treatment had the highest incidence rate of excessive sedation (16%), whereas endoscopic ultrasound-guided intervention had the lowest incidence rate (4.3%). Multivariate analysis revealed significant associations between excessive sedation and comorbid sleep apnea, obesity, and prolonged procedural time. Obesity, sleep apnea syndrome, and prolonged procedure time are risk factors for excessive sedation related to propofol use. Thus, sedation techniques should be tailored for these patients.