Obesity is advancing at an accelerated pace and yet its treatment is still an emerging field. Although studies have demonstrated the role of the microbiota in the pathogenesis of obesity, this is the first study to show the effects of intermittent fasting (IF), combined or not with exercise (HIIT), on the gut microbiota composition in women with obesity. Our hypothesis is that IF combined with HIIT can promote the remodeling of the composition and function of the gut microbiota. Thirty-six women with obesity participated in the study, aged between 18 and 40 years, randomly divided into 3 groups: 1) IF associated with HIIT group (IF+EX, n = 15); 2) HIIT group (EX, n = 11); and 3) IF group (IF, n = 10). Interventions took place over 8 weeks and all assessments were performed pre- and post-intervention. The HIIT circuit was performed 3x/week, for 25 minutes/session. The IF protocol was a 5:2 (2x/week). Multiplex analysis of inflammatory cytokines, sequencing of the 16S rRNA gene, and gas chromatography to measure fecal concentrations of short-chain fatty acids (SCFAs) were performed. This study was registered on ClinicalTrials.gov (NCT05237154). Exercise increased fecal acetate concentrations ( P = 0.04), but no changes were observed in the composition and functional profile of the microbiota. The interventions did not change the composition of the microbiota, but exercise may play a modulatory role in the production of acetate. This investigation provides clinical insights into the use of IF and HIIT for women with obesity.