Scopel‐Theanine (l‐Thea) is an amino acid which is naturally present in tea leaves. It has been associated with possible health advantages, including obesity prevention, but the underlying molecular mechanisms have not been elucidated.Methods and resultsA multiomics approach is utilized to examine the mechanism by which l‐Thea exerts its antiobesity effects. This study reveals that l‐Thea administration significantly ameliorates high‐fat diet (HFD)‐induced obesity in rats by improving body weight and hyperlipidemia. l‐Thea mitigates HFD‐induced inflammation and reverses hepatic and colonic damage, and intestinal barrier. This research verifies that the preventive effect of l‐Thea on obesity in rats induced by an HFD with colitis is accomplished by suppressing the phosphorylation of important proteins in the NF‐κB/mitogen‐activated protein kinase (MAPK) pathways. Metabolome analysis reveals that l‐Thea regulates HFD‐induced metabolic disorders, specifically through modulation of steroid hormone biosynthesis. Microbiome analysis reveals that l‐Thea mitigates HFD‐induced dysbiosis by increasing the relative abundance of obesity‐associated probiotic bacteria, including Blautia coccoides and Lactobacillus murinus, while simultaneously suppressing the abundance of pathogenic bacteria.Conclusionsl‐Thea alleviates colitis generated by an HFD by restoring the integrity of the intestinal barrier, suppressing inflammation through regulation of MAPK/NF‐κB signaling pathways, and enhancing microbial metabolism in colon.