Objective <p>Obesity and body composition are shaped by both genetic and lifestyle factors. This study examined the effect of the FTO rs9939609 polymorphism on body composition in women, with attention to physical activity levels.</p> Methods <p>A cross-sectional study included 360 women aged 18 to 69 years. The genotyping of FTO rs9939609 was performed by real-time polymerase chain reaction. Anthropometric and bioelectrical impedance analyses were used to assess body composition.</p> Results <p>The frequency of FTO risk allele A was 45.3%, with AT being the most common genotype (43.9%). No significant differences in allele or genotype frequencies were observed between recreationally active and inactive women. Across the cohort, carriers of at least one A allele tended to have higher body fat and lower skeletal muscle mass. Among women with risk genotypes (AA and AT), recreational athletes displayed more favorable body composition, with lower fat mass and percentage, higher total body water, and a more advantageous fat mass–to–fat-free mass ratio than non-athletes. After correction for multiple comparisons, these four indicators remained statistically significant. Waist-to-height ratio was the strongest anthropometric predictor of adiposity, while body fat percentage and the fat mass–to–fat-free mass ratio were most informative in bioimpedance analysis.</p> Conclusions <p>Recreational physical activity is associated with a more favourable body composition in women with the FTO risk allele, suggesting that it mitigates the genetic susceptibility to adiposity. Integrating anthropometric and bioimpedance measures can improve the evaluation of adiposity, and standardised body fat evaluation should be incorporated into routine obesity screening.</p>