Early diagnosis of colorectal cancer substantially improves survival. However, over half of cases are diagnosed late due to the demand for colonoscopy—the ‘gold standard’ for screening—exceeding capacity. Colonoscopy is limited by the outdated design of conventional endoscopes, which are associated with high complexity of use, cost and pain. Magnetic endoscopes are a promising alternative and overcome the drawbacks of pain and cost, but they struggle to reach the translational stage as magnetic manipulation is complex and unintuitive. In this work, we use machine vision to develop intelligent and autonomous control of a magnetic endoscope, enabling non-expert users to effectively perform magnetic colonoscopy in vivo. We combine the use of robotics, computer vision and advanced control to offer an intuitive and effective endoscopic system. Moreover, we define the characteristics required to achieve autonomy in robotic endoscopy.