Display omitted •HSE improved diet-induced obesity-associated inflammation in mice.•This study shows for the first time that HSE modulates the microbiota in obese mice.•Administration of HSE ameliorated gut dysbiosis in diet-induced obesity in mice.•Prebiotic properties of HSE could mediate its beneficial effects in obesity.•HSE could be developed as a potential functional food for the metabolic syndrome. The metabolic syndrome has been associated with an alteration of intestinal microbiota, which can be considered as a target for the management of these patients. Phenolic extracts from Hibiscus sabdariffa have shown beneficial effects on obesity and its related complications. However, their effects on gut microbiota have not been investigated yet. This study evaluates the effects of a chemically characterized polyphenolic extract of H. sabdariffa (HSE) in an experimental model of diet-induced obesity (DIO) in mice. HSE was administered daily by oral gave for 42 days. HSE reduced weight increase in high fat diet (HFD)-fed mice, and improved glucose tolerance, insulin sensitivity and normalized LDL/HDL cholesterol ratio. It also enhanced the inflammatory state in the liver, reducing the expression of different adipokines and proinflammatory mediators, and reinforced gut integrity by increasing the expression of mucins and proteins involved in the maintenance of mucosal barrier. Moreover, HSE had a prebiotic effect, ameliorating the changes in the gut microbiota induced by the HFD. Thus, HSE improved the Firmicutes/Bacteroidetes ratio, which may contribute to the beneficial effects. Consequently, HSE could be considered for the development of a complementary treatment for the metabolic syndrome due to its beneficial properties.