Structural alterations in the gut microbiota (GM) are closely linked to aging and age-related diseases. Although exercise may improve health in older adults by modulating gut microecology, its specific effects on GM lack systematic evaluation.

To systematically assess the effects of exercise interventions on GM diversity and characteristic microbial genera in older adults.

PubMed, Embase, the Cochrane Library, and Web of Science were searched from inception to December 2025 and updated in February 2026. Eligible studies included trials evaluating the effects of exercise interventions on gut microbiota in older adults. Risk of bias and evidence certainty were assessed using the Cochrane Risk of Bias 2.0 tool and the GRADE framework, respectively. Random-effects models were used to calculate Hedges’ g. Subgroup analyses, meta-regression, and restricted cubic spline dose–response analyses were performed.

Sixteen studies were included. Exercise significantly increased α-diversity, reflected by improvements in the Shannon index (g = 0.22, 95% CI: 0.06–0.38, P = 0.007) and Chao1 index (g = 0.22, 95% CI: 0.08–0.35, P = 0.002). The Observed index showed marginal significance ( P = 0.052), whereas the Simpson index was unchanged. Moderate-intensity exercise demonstrated a stronger effect (g = 0.38, 95% CI: 0.18–0.58), with greater benefits in males and individuals with higher BMI. Meta-regression suggested a negative age–effect trend (β = −0.0238, P = 0.079). A significant inverted U-shaped dose–response relationship was observed for the Shannon index (non-linear P = 0.0226), with optimal effects at 700–900 METs/week. No significant changes were found in the two dominant phyla or Bifidobacterium; however, Akkermansia increased (g = 0.60, 95% CI: 0.29–0.92, P < 0.001) and Escherichia decreased (g = −0.64, 95% CI: −1.20 to −0.08, P = 0.026).

Exercise enhances α-diversity and modulates specific genera while maintaining core GM stability in older adults, with dose-dependent effects requiring confirmation in longitudinal studies.