Abstract Background Optimal patient education prior to colonoscopy improves adherence to instructions for bowel preparation and leads to cleaner colons. We developed computer-based education (CBE) supported by video and 3 D animations. We hypothesized that CBE could replace nurse counselling without loss of bowel preparation quality during colonoscopy. Methods We conducted a prospective, multicenter, endoscopist-blinded, non-inferiority randomized controlled trial. The primary outcome was adequate bowel preparation, evaluated using the Boston Bowel Preparation Scale (BBPS). Secondary outcome measures were: sickness absence for outpatient clinic visits; patient anxiety/satisfaction scores; and information recall. We included patients in four endoscopy units (rural, urban, and tertiary). Results We screened 1035 eligible patients and randomized 845. After evaluation, 684 were included in the intention-to-treat (ITT) group. Subsequently, 497 patients were included in the per-protocol analysis, 217 in the nurse counselling and 280 in the CBE group. Baseline characteristics were similarly distributed among the groups. On per-protocol analysis, adequate bowel cleansing was achieved in 93.2 % (261/280) of CBE patients, which was non-inferior to nurse-counselled patients (94.0 %; 204/217), with a difference of −0.8 % (95 % confidence interval [CI] −5.1 % to 3.5 %). Non-inferiority was confirmed in the ITT population. Sickness absence was significantly more frequent in nurse-counselled patients (28.0 % vs. 4.8 %). In CBE patients, 21.5 % needed additional information, with 3.0 % needing an extra outpatient visit. Conclusion CBE is non-inferior to nurse counselling in terms of bowel preparation during colonoscopy, with lower patient sickness leave. CBE may serve as an efficient educational tool to inform patients before colonoscopy in routine clinical practice.