Approximately 30% of patients with quiescent inflammatory bowel disease (IBD) meet the diagnostic criteria for irritable bowel syndrome (IBS). The aim of this study was to evaluate the effectiveness of a low-FODMAP diet in patients who meet the diagnostic criteria for IBS whilst in IBD remission. A total of 200 patients in remission of IBD were included in the study. Sixty-five of these patients (32.5%) were diagnosed with IBS according to the R4DQ. On the patients who met the IBS diagnostic criteria, anthropometric measurements, laboratory tests and lactulose hydrogen breath tests were performed. A low-FODMAP diet was introduced for 6 weeks. Of the 59 patients with IBS diagnosed at baseline for whom data were collected at the end of follow-up, after the low-FODMAP intervention IBS-like symptoms were not present in 66.1% (n = 39) (95% CI (53.4%; 76.9%)). The difference between the two groups (with SIBO at baseline (33 of 48 patients) and without SIBO at baseline (6 of 11 patients)) in the low-FODMAP diet's effectiveness was not statistically significant (p = 0.586). The low-FODMAP diet improved the gut symptoms of flatulence and diarrhea. It had no effect on the occurrence of constipation. In IBD patients in remission who meet the IBS criteria, the dietary intervention of a low-FODMAP diet is effective for a reduction in IBS-like symptoms, regardless of the coexistence of bacterial overgrowth.