BACKGROUND: No conclusive treatment is available for irritable bowel disease (IBD). Adherence to a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) might alleviate clinical symptoms of IBD. However, no study has investigated the effect of low FODMAPs diet on the intestinal microbiota and inflammatory biomarkers in patients with IBD. The aim of current study is to examine the effect a low FODMAP diet on IBD symptoms, inflammation, and the intestinal microbiota in patients with ulcerative colitis. METHODS AND ANALYSIS: This study is a randomized clinical trial. Thirty patients with mild to moderate ulcerative colitis will be randomly allocated to receive a low FODMAP diet (n = 15) or to continue their usual diet as control (n = 15), for 4 weeks. The quantity of intestinal microbiota including Clostridium cluster IV, Faecalibacterium prausnitzii, Rosburia spp., Lactobacillus spp., Bifidobacteria spp., Akkermansia muciniphila, Bacteroides fragilis, and Ruminococcus spp., and the Firmicutes to Bacteroidetes ratio and calprotectin and lactoferrin levels will be explored in fecal samples from patients. In addition, anthropometric measures and biochemical assessments including serum concentrations of highly sensitive-C reactive protein (hs-CRP), tumour necrosis factor-α (TNF-α) and IL-1β will be taken from patients at baseline and end of the study. The study has been registered in IRCT (IRCT20181126041763N1; registration date: 2019-01-18). DISCUSSION: Consumption of a low-FODMAP diet might decrease systemic and intestinal inflammation, change the bacterial population in the gut, and modulate clinical symptoms in patients with ulcerative colitis. Further studies investigating the effect of such a diet on other variables, including other bacterial species and inflammatory cytokines, are required to confirm future findings of this trial.