Background <p>The gut microbiota plays a substantial role in obesity. Glucagon-like peptide-1 receptor agonists (GLP-1RAs) can affect body weight, insulin resistance, and lipid metabolism via combined hypothalamic feeding centre and gastrointestinal tract activity. It also affects the intestinal flora of patients with obesity. We investigated changes in visceral fat and gut microbiota of patients with obesity treated with beinaglutide.</p> Methods <p>Thirty-three patients from our hospital with obesity treated with beinaglutide and 20 sex- and age-matched healthy controls were included based on the inclusion and exclusion criteria. Glycolipid metabolism indices, inflammation indices, and hepatic and renal functions were assessed at treatment initiation and 4 and 12&#xa0;weeks after treatment. Body weight, waist circumference, blood pressure, and body composition (visceral fat area, body fat, body fat percentage, skeletal muscle, and basal metabolic rate) were measured. The Homeostatic Model Assessment of Insulin Resistance index was calculated. Fecal samples were collected from 12 cases. Effects on intestinal flora were assessed by sequencing the V3–V4 region of the 16S rRNA gene.</p> Results <p>Beinaglutide significantly reduced visceral fat area, improved glycolipid metabolism, and decreased total cholesterol, low-density lipoprotein cholesterol, blood glucose, and C-reactive protein levels. It also considerably restored the α-diversity of intestinal flora, with decreased in relative abundances of <i>Prevotella</i>, <i>Lachnospira and Dialister</i> at the genus level and increased in the relative abundance of <i>Blautia A</i> and <i>Gemmiger A</i>.</p> Conclusions <p>Our findings provide insights into the mechanisms by which beinaglutide aids weight loss, particularly via modulating the gut microbiota.</p> Graphical abstract <p></p>