BACKGROUND: Opinions about the impact of bowel preparation on the gut microbiota are divided. This study investigated the effects of different regimens on the gut microbiota post-bowel preparation and the differences in responses across different age groups. METHODS: This single-center, prospective, randomized, controlled clinical trial included 194 patients. Patients were categorized into two groups: one group receiving polyethylene glycol (n = 108) and one receiving sodium picosulfate (n = 86) for bowel preparation. Fecal samples were collected at baseline and on days 7 and 14 post-bowel preparation. The microbiota's diversity and composition were analyzed using 16S ribosomal RNA gene sequencing, followed by comparative analyses. RESULTS: The gut microbiota's abundance and diversity in patients significantly decreased post-bowel preparation, which did not recover to the level of pre-bowel preparation on Day 14. When comparing different regimens, the polyethylene glycol and sodium picosulfate groups recovered faster in richness and diversity, respectively. Patients aged <
65 years had higher richness and diversity of the gut microbiota, whereas the microbiota structure in those aged ≥ 65 years returned to the baseline state faster. The structure of beta diversity is significantly altered and did not return in the short term. However, in the elderly population aged ≥ 65 years, it can rebound quickly. This study also identified a number of significantly altered bacterial genera. CONCLUSIONS: Following the use of different bowel preparation regimens, the gut microbiota recovers in diverse ways, with older people over 65 experiencing a faster recovery of the microbial structure.