Fecal volatile organic compounds (VOCs) offer insights into gut microbiota function that may drive the pathogenesis of ulcerative colitis (UC). This cross-sectional study aimed to compare dietary intake and VOC patterns in UC patients with an ileoanal pouch compared to those with an intact colon. Seven-day food records and fecal samples were collected from UC patients with an intact colon (n = 28) or an ileoanal pouch (n = 11). Fecal VOC profiles were analyzed using gas chromatography-mass spectrometry. Dietary intake in both groups was largely similar. The mean Jaccard similarity index of VOC was 0.55 (95% CI:0.53, 0.56) in the pouch compared with 0.48 (0.47, 0.49) in the colon group (p < 0.01). A lower proportion of VOC classes was detected in the pouch, including sulfide (9% vs. 57%; p < 0.01), branched-chain fatty acids (BCFAs; 45%-64% vs. 93%-96%; p < 0.01), and ketones (45%-64% vs. 93%-96%; p < 0.01), along with a higher proportion of butyric acid (91% vs. 29%; p < 0.001). Unrelated to diet, VOC profiles show less functional diversity, reduced protein and greater carbohydrate fermentation, and altered production of secondary metabolites in the UC-pouch compared with the intact colon. These differences in the metabolic environment of the gut microbiota provide insights into pathogenesis and suggest that microbial-targeted interventions should be tailored accordingly.