Abstract Background The concept of Treat to Target and Tight Control relies heavily on bowel mucosa assessment. This implies that multiple endoscopies should be performed for any patient with moderate to severe inflammatory bowel disease (IBD). Improving patient tolerance of bowel preparation is important as we stride for frequent endoscopic monitoring. We aimed to compare low-volume (2 litres) Sodium Picosulfate (Pico) and high-volume (4 litres) Polyethylene Glycol (PEG) bowel preparation regimens, as well as split dosing, in terms of tolerance, efficacy and safety. Methods We included all adult IBD patients of our IBD clinic who underwent colonoscopy in the last 2 years for the sole purpose of mucosal healing assessment. We excluded patients with an indication of cancer surveillance, acute severe colitis, bowel strictures with obstructive symptoms, and patients with renal or liver failure. We used a Visual Analog Scale (VAS) assessed by patients to evaluate tolerance, and Boston Bowel Preparation Scale (BBPS) assessed by physicians to evaluate efficacy. Results A total of 139 patients were included in the study: 70 (50,4%) male patients, 86 (61,8%) with Crohn’s disease and 53 (38,2%) with ulcerative colitis, with a mean age of 46,14 years (range 17–74) and mean disease duration of 10.12 years. We included 21 patients (15.1%) with a previous ileocecal resection. Low-volume Pico preparation was received by 48 (34,5%) patients. High-volume PEG preparation was received by 91 (65,5%) patients. Split dosed preparation was received by 49 (35.2%) patients. Low-volume Pico preparation was significantly better tolerated than high-volume PEG preparation (VAS 81,75 vs. 65,69, p < 0,001) without a negative impact on bowel preparation quality (BBPS 7,65 vs. 7,32, p = 0.237). Split dosing did not improve tolerance (VAS 74,96 vs. 67,75, p = 0.221) but it improved the quality of the preparation (BBPS 7,94 vs. 7.13, p = 0,002). No meaningful differences were observed in terms of isolated aphthous ulcers (0% vs. 4%, p = 0,325). Complete intake of preparation was significantly higher in the low-volume Pico group (94,7% vs. 74,7%, p = 0,002). Complete colonoscopy was achieved in all patients. No serious adverse events related to the bowel preparation were reported. Patients in the low-volume Pico group were slightly younger (42,54 vs. 48,03 years, p = 0,034) and more likely to have had surgery (25% vs. 9,9%, p = 0,018). Conclusion Although this was a single-centre non-randomised study with a relatively small number of patients, it clearly demonstrated that low-volume PICO split dosed bowel preparation is superior for IBD patients scoped to check for endoscopic remission, as it improves tolerance and quality without compromising efficacy. Further evidence from randomised studies is needed.