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, and high-intensity interval training (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, aged between 18 and 40 yr, participated in the study. They were randomly divided into three groups: 1) IF associated with HIIT group [IF + exercise group (EX), n = 15]; 2) HIIT group (EX, n = 11); and 3) IF group (IF, n = 10). Interventions took place over 8 wk, and all assessments were performed preintervention and postintervention. The HIIT circuit was performed 3 times/wk, for 25 min/session. The IF protocol was a 5:2 (2 times/wk). 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.NEW & NOTEWORTHY This is the first investigation about alternate-day fasting combined with HITT on the gut microbiota of obese women. The study contributes to the advancement of human science involving IF and HIIT, popular strategies for managing obesity. Previous evidence has explored IF in modulating the microbiota in animal models or specific populations and clinical conditions. Despite the subtle outcomes, this study has relevance and originality in the field of gut microbiota knowledge.