Objective Obesity is associated with impaired gut microbiota diversity, which has been linked to the development of type 2 diabetes. This study aims to examine the effects of an 8‐week aerobic exercise intervention on insulin sensitivity, visceral adiposity, and gut microbiota diversity and composition in participants with obesity. Methods Fourteen participants (mean SD, age 51 11 years; BMI 34.9 4.9 kg/m2) performed an 8‐week exercise intervention (2 to 4 times/week on 65% to 85% of heart rate reserve). Insulin sensitivity (hyperinsulemic euglycemic clamp), cardiorespiratory fitness (maximal oxygen uptake), visceral adiposity (dual‐energy X‐ray absorptiometry scan) and gut microbiota composition (16S rRNA gene sequencing) were measured before and after the intervention. Results Insulin sensitivity showed a significant increase (pre: 3.8 1.9 mg/min/kg; post: 4.5 1.7 mg/min/kg; p = 0.007) after training, whereas visceral adiposity decreased (pre: 959 361 cm3; post: 897 364 cm3; p = 0.02). No change in gut microbiota α‐ or β‐diversity was found. At the genus level, the abundance of Ruminococcus gauvreauii (p = 0.02); Lachnospiraceae FCS020 group (p = 0.04), and Anaerostipes (p = 0.04) significantly increased after exercise training. Significant positive correlations were present for M‐value (R. gauvreauii) and VO2 max (R. gauvreauii and Anaerostipes). Conclusions Eight‐week exercise training in humans with obesity leads to marked improvements in insulin sensitivity and body composition and is accompanied by modest changes in 3 gut microbiome genera, all belonging to the Firmicutes phylum.