Colonoscopy is the gold standard for diagnosing and monitoring gastrointestinal diseases. However, bowel preparation, rather than the procedure itself, appears to be the main driver of transient gut microbiota disruption. Available evidence suggests that microbiota alterations after bowel preparation and colonoscopy may persist for days to weeks and may be associated with changes in barrier function, microbial metabolism, and symptom burden in susceptible individuals. This review summarizes current knowledge on the mechanisms underlying microbial disruption induced by bowel preparation, including loss of diversity, shifts in key taxa, impairment of metabolic pathways, and alterations in immunomodulatory metabolites. It also discusses potential clinical consequences and highlights nutritional strategies that may support microbiota recovery, including dietary fiber, polyphenols, and microbiota-targeted approaches. This review also highlights current research gaps and the need for well-designed clinical studies in this field.