Monitoring complications of colonoscopies after a positive faecal immunochemical test (FIT-colonoscopies) is crucial in FIT-based colorectal cancer (CRC) screening. We investigated the occurrence of bleeding and perforation post FIT-colonoscopies (2013–2019) in Flanders and the contributing factors. A retrospective case–control study was conducted, including bleeding/perforation cases within 14 days after index colonoscopy, and controls without such events. Bleeding rates dropped from 0.9–1.1% (pre-2017) to 0.3% (2017–2018) and further to 0.05% (2019), while perforation rates remained at 0.05–0.11% (2014–2019). Male gender, polypectomy, general anaesthesia, and recent antiplatelet/antithrombotic drug use increased bleeding odds. Incomplete colonoscopy, polypectomy, general anaesthesia, and recent antiplatelet/antithrombotic drug use raised perforation odds. The endoscopists (n = 16) with highest bleeding rates (top 5%) performed only 6% of total FIT-colonoscopies, yet their patients experienced 45.5% of bleeding events. Similarly, for the top 5% of perforation rates, endoscopists conducting only 4.5% of total FIT-colonoscopy had 49.0% of perforation events occur in their patients. This study sheds light on FIT-colonoscopy-related complications in Flanders, their rates and risk factors. These findings can be incorporated into CRC screening materials and guide interventions to mitigate complications. A central colonoscopy register is currently lacking in Belgium, highlighting the need for its establishment to facilitate recurrent monitoring and evaluation.