Alterations of the gut microbiome have been associated with obesity and metabolic disorders. The gut microbiota can be influenced by the intake of dietary fibres with prebiotic properties, such as inulin-type fructans. This study tested the hypothesis that obese individuals subjected for 12 weeks to a inulin-enriched versus inulin-poor diet have differential faecal fermentation patterns. The fermentation of cellulose and inulin hydrolysates, of six different inulin-rich and inulin-poor vegetables of both groups was analysed in vitro on faecal inocula. The results showed that the microbiota from obese patients who received fructan-rich diet for three weeks produce more gas and total short-chain fatty acid (SCFA) compared to the microbiota taken of the same individuals before the treatment. Obese individuals fed with a low-fructan diet produce less gas and less SCFA compared to the treated group. This study highlighted profound changes in microbiota fermentation capacity obtained by prebiotic intervention in obese individuals, which favors the production of specific bioactive metabolites.