A 12‑week course of semaglutide (starting at 0.25 mg then 0.5 mg weekly) in obese people with type‑2 diabetes and fatty liver cut weight, lowered blood sugar, reduced liver stiffness and inflammation, and shifted blood metabolites toward more beneficial fats and amino‑acid profiles.

<b>Objective:</b> To investigate the effect of semaglutide on the metabolomics of obese patients with type 2 diabetes mellitus (T2DM) complicated by metabolic-associated fatty liver disease (MAFLD). <b>Methods:</b> A prospective non-randomized controlled study was conducted. Obese patients with T2DM complicated by MAFLD who attended the Department of Endocrinology of Shijiazhuang People's Hospital from October 2022 to June 2023 were selected as the semaglutide group, and healthy individuals from the physical examination center were selected as the control group. Clinical data of both groups were collected. The semaglutide group was subcutaneously injected with semaglutide following a basic hypoglycemic regimen (starting dose of 0.25 mg once a week, which was changed to 0.5 mg once a week after 1 week for 12 weeks). Liquid chromatography-tandem mass spectrometry was used for qualitative and quantitative analyses of plasma metabolites, and multivariate analysis methods were used to analyze the metabolomics data. <b>Results:</b> In total, 69 patients in the semaglutide group completed the treatment, with 49 males (71%) and a median age of 46 (36, 54) years, and the healthy control group consisted of 100 individuals, with 38 males (38%) and a median age of 40 (35, 45) years. The body mass index and levels of fasting blood glucose, alanine aminotransferase, and interleukin-6 (IL-6) in the semaglutide group before treatment were significantly higher than those in the control group (all <i>P</i>&lt;0.001). The body mass index [23.65 (22.33, 24.45) vs. 28.72 (27.50, 32.07) kg/m²], liver stiffness measurement [1.61 (0.91, 2.00) vs. 5.78 (5.51, 6.10) kPa], and homeostasis model assessment of insulin resistance index [5.10 (2.90, 7.95) vs. 9.00 (6.25, 11.80)] in the semaglutide group were significantly lower after treatment than before treatment (all <i>P</i>&lt;0.001), and the blood glucose, blood lipid, liver function indicator, and IL-6 levels all significantly decreased after treatment. Metabolomics analysis revealed that there were 219 differential metabolites (131 up-regulated and 88 down-regulated) between the semaglutide group (<i>n</i>=27) before treatment and the control group (<i>n</i>=12), with glycerophospholipids and free fatty acids being significantly up-regulated. The semaglutide group showed 203 differential metabolites (121 up-regulated and 82 down-regulated) after treatment compared with before, with significant down-regulation of long-chain fatty acids and significant up-regulation of metabolites including carnitines, branched-chain amino acids, and taurine. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the differential metabolites identified before and after semaglutide treatment were involved in several signaling pathways, such as biosynthesis of unsaturated fatty acids, linoleic acid metabolism, aldosterone synthesis and secretion, and the mTOR signaling pathway, etc. <b>Conclusion:</b> Semaglutide alters the serum metabolite levels in obese patients with T2DM complicated by MAFLD.