Background: Emerging evidence highlights the bidirectional interaction between physical activity and the gut microbiota, which plays a critical role in host metabolism, immune modulation, and intestinal barrier integrity. Understanding how different forms of exercise influence gut microbiota is essential for optimizing health strategies based on lifestyle interventions. Methods: A systematic literature review was conducted using databases including PubMed, Scopus, ScienceDirect, and Google Scholar for articles published from January 2019 to July 2025. Inclusion criteria covered human studies with microbiota outcomes assessed via 16S rRNA or shotgun metagenomics sequencing. Animal studies, non-English articles, and reviews without primary data were excluded. Results: Moderate-to-high intensity aerobic exercise performed consistently for at least 2 weeks was associated with increased microbial diversity and enrichment of SCFA-producing bacteria. Exercise also upregulated tight junction proteins, suggesting improved intestinal barrier function. However, responses varied depending on exercise type, duration, individual metabolic status, and diet. Excessive training without adequate recovery may induce dysbiosis and inflammation. Conclusion: Physical activity positively influences gut microbiota composition and barrier function, with potential systemic benefits for metabolic, gastrointestinal, and neurological health. Personalized exercise prescriptions, integrated with dietary and lifestyle factors, may serve as effective strategies for microbiota-targeted interventions in health promotion and disease prevention.