Participants of the FMT group experienced a significant and sustained reduction in the A/G fat ratio at 6, 12, and 26 weeks compared to placebo (all p < 0.05).No significant effects were found on insulin sensitivity, liver enzymes, lipid profile, inflammatory markers, total body fat percentage, or quality of life (all p > 0.05).In children with metabolic syndrome at baseline, FMT was associated with a significantly higher resolution rate of the condition by week 26 (from 18 to 4 cases) compared to placebo (from 13 to 10 cases), with an aOR of 0.06 (95% CI 0.01–0.45; p = 0.007). Here, INS is linked to metabolic syndrome.