Background Ulcerative colitis (UC) is a chronic inflammatory bowel disease marked by mucosal inflammation and disruption of gut microbial homeostasis. Emerging evidence highlights the significance of gut microbiota-derived metabolites, including short-chain fatty acids (SCFAs) and tryptophan derivatives, in modulating intestinal inflammation and mucosal integrity. Objective To investigate the concentrations of key gut microbial metabolites in UC patients and evaluate their association with histological inflammation severity Methodology a cross-sectional study was conducted on 110 patients diagnosed with UC. Baseline clinical data were recorded, including disease duration, severity (based on histology using the Geboes scoring system), and medication history. Fecal samples were analyzed for levels of butyrate, propionate, acetate, indole-3-propionic acid (IPA), deoxycholic acid (DCA), and trimethylamine-N-oxide (TMAO) using standard biochemical methods. Correlations between metabolite levels and mucosal inflammation scores were analyzed using Pearson’s correlation, and comparisons across severity groups were assessed with Mann-Whitney U and ANOVA tests. Results The mean levels of butyrate (8.9 ± 2.1 µmol/g), propionate (6.5 ± 1.6 µmol/g), and IPA (2.0 ± 0.6 µmol/g) were significantly below normal reference ranges. Butyrate and IPA showed moderate to strong negative correlations with histological inflammation (r = –0.54 and –0.62; p < 0.001). TMAO was positively correlated with inflammation severity (r = 0.31, p = 0.002) and significantly elevated in moderate/severe cases (6.1 ± 1.9 µmol/g vs. 4.8 ± 1.6 µmol/g, p = 0.006). Conclusion UC patients exhibited reduced levels of beneficial microbial metabolites, particularly SCFAs and IPA, which were inversely associated with inflammation severity. These findings support the potential role of microbiota-targeted therapies in UC management.