Introduction In the UK, endoscopy certification is administered by the Joint Advisory Group on Gastrointestinal Endoscopy (JAG). Since 2011, certification for upper and lower gastrointestinal endoscopy has been awarded via a national (JETS) e-portfolio to the main training specialties of: gastroenterology, gastrointestinal surgeons (GS) and non-medical endoscopists (NME). Trends in endoscopy certification and differences between trainee specialties were analyzed. Methods This prospective UK-wide observational study identified trainees awarded gastroscopy, sigmoidoscopy, colonoscopy (provisional and full) certification between June 2011 - 2017. Trends in certification, procedures and time-to-certification, and key performance indicators (KPIs) in the 3-month pre- and post-certification period were compared between the three main training specialties. Results Three thousand one hundred fifty-seven endoscopy-related certifications were awarded to 1928 trainees from gastroenterology (52.3 %), GS (28.4 %) and NME (16.5 %) specialties. During the study period, certification numbers increased for all modalities and specialties, particularly NME trainees. For gastroscopy and colonoscopy, procedures-to-certification were lowest for GS ( P < 0.001), whereas time-to-certification was consistently shortest in NMEs ( P < 0.001). A post-certification reduction in mean cecal intubation rate (95.2 % to 93.8 %, P < 0.001) was observed in colonoscopy, and D2 intubation (97.6 % to 96.2 %, P < 0.001) and J-maneuver (97.3 % to 95.8 %, P < 0.001) in gastroscopy. Overall, average pre- and post-certification KPIs still exceeded national minimum standards. There was an increase in PDR for NMEs after provisional colonoscopy certification but a decrease in PDR for GS trainees after sigmoidoscopy and full colonoscopy certification. Conclusion Despite variations among trainee specialties, average pre- and post-certification KPIs for certified trainees met national standards, suggesting that JAG certification is a transparent benchmark which adequately safeguards competency in endoscopy training.