<p>In gastrointestinal endoscopy, the ability to perform increasingly complex procedures has significantly heightened the demand for effective team cooperation. Crew Resource Management (CRM) and Threat and Error Management (TEM), proven strategies from civil aviation, have the potential to enhance team communication, workflow and patient outcomes in complex medical settings such as interventional endoscopy and therefore were implemented into endoscopy unit in this study. Together with qualified CRM trainers, individually tailored CRM and TEM elements such as communication guidelines, checklists and TEM-based dialogic team-time-outs were developed with the employees and integrated into endoscopic workflow at a high-volume interventional endoscopy center. Employee surveys on the effects were performed before and after the implementation. Implementation of CRM and TEM elements into endoscopy with civil aviation experts improved team communication, workflow and teamwork in endoscopy. Our study found a significantly reduced rate of misunderstandings caused by ambiguous communication during endoscopic interventions (<i>p</i> = 0.034), a significantly clearer defined distribution of tasks during the procedure (<i>p</i> = 0.020) and a significantly improved physicians’ information transfer to the nursing assistants before the procedure (<i>p</i> = 0.047). More than 80% of all employees perceived that patient safety had improved after the intervention.</p>