Abstract Background Current guidelines regarding surveillance after screening colonoscopy assume adequate bowel preparation. However, follow-up intervals after suboptimal cleansing are highly heterogeneous. We aimed to determine the diagnostic yield of early repeat colonoscopy in patients with suboptimal bowel preparation in fecal immunochemical test (FIT)-based screening colonoscopy. Methods An observational study including patients who underwent colonoscopy with suboptimal bowel preparation after positive FIT screening and then repeat colonoscopy within 1 year. Suboptimal preparation was defined as a Boston Bowel Preparation Scale (BBPS) score of 1 in any segment. Patients with a BBPS score of 0 in any segment or incomplete examination were excluded. The adenoma detection rate (ADR), advanced ADR (AADR), and colorectal cancer rate were calculated for the index and repeat colonoscopies. Results Of the 2474 patients with FIT-positive colonoscopy at our center during this period, 314 (12.7 %) had suboptimal preparation. Of the 259 (82.5 %) patients who underwent repeat colonoscopy, suboptimal cleansing persisted in 22 (9 %). On repeat colonoscopy, the ADR was 38.7 % (95 %CI 32.6 % to 44.8 %) and the AADR was 14.9 % (95 %CI 10.5 % to 19.4 %). The per-adenoma miss rate was 27.7 % (95 %CI 24.0 % to 31.6 %), and the per-advanced adenoma miss rate was 17.6 % (95 %CI 13.3 % to 22.7 %). After repeat colonoscopy, the post-polypectomy surveillance recommendation changed from 10 to 3 years in 14.7 % of the patients with previous 10-year surveillance recommendation. Conclusions Patients with suboptimal bowel preparation on FIT-positive colonoscopy present a high rate of advanced adenomas in repeat colonoscopy, with major changes in post-polypectomy surveillance recommendations.