Some individual fruits have been widely researched for their effects on overall health and correlations with chronic diseases. The beneficial effects of mango supplementation on metabolic diseases have been detected. However, research into mango consumption on gut health, including the microbiome, is limited to processed mango preparations or peels. Our goal was to examine the effects of fresh mango consumption on the gut microbiome, gut permeability proteins, and bowel movement habits in overweight/obese individuals. In a 12‐week crossover design study, 27 participants consumed 100 kcal/day of either mangos or low‐fat cookies with a washout period of 4 weeks. The mango intervention showed higher Shannon–Wiener and Simpson alpha diversity indices of the microbiome than the low‐fat cookie intervention in week 4. Significant differences in beta diversity of the microbiome were found between diet interventions at week 12. Mango consumption increased the abundance of Prevotella maculosa, Corynebacterium pyruviciproducens, and Mogibacterium timidum while it decreased Prevotella copri. Low‐fat cookie intake increased Cyanobacterium aponinum and Desulfovibrio butyratiphilus and reduced Alloscardovia omnicolens. There were no significant differences in circulating gut permeability protein (ZO‐1, claudin‐2, and occludin) levels. There was a slight increase in the amount of bowel movement with mango consumption, but no significant findings for frequency, consistency, strain, pain, and constipation in bowel movement between trials. Given these results, it can be concluded that consumption of mango may have positive effects on the gut health, which may yield possible health benefits for chronic disease that deserve further study.