The gut microbiome plays a critical role in adaptation to exercise through the gut-muscle axis, influencing metabolic regulation, immune homeostasis, gut barrier integrity, and recovery. However, evidence regarding exercise-induced changes in the gut microbiome of athletes remains inconsistent because microbial responses depend on the training modality, intensity, and duration. This narrative review provides a comprehensive overview of the available evidence on exercise-induced gut microbiome modulation in athletes, explores the underlying mechanisms of the gut-muscle axis, and evaluates their implications for exercise performance, recovery, and overall health. The reviewed literature was identified through searches in PubMed, Scopus, Web of Science, and Google Scholar. Existing evidence suggests that athletes generally exhibit greater gut microbial diversity and a greater abundance of beneficial microbial species than sedentary individuals. Moderate-intensity exercise consistently enhances short-chain fatty acid-producing bacteria, improves intestinal barrier function, increases metabolic flexibility, and reduces systemic inflammation, whereas prolonged or high-intensity exercise may induce gut dysbiosis, increase intestinal permeability, and worsen gastrointestinal symptoms. Overall, the available evidence supports the beneficial role of exercise in shaping the gut microbiome and its potential contribution to athletic performance and recovery. However, future research using standardized methods and specific athletic populations is warranted to elucidate more precise and evidence-based mechanisms.