Abstract Background This study explored relationships between gut microbiome, faecal calprotectin (FCP) and an adapted Canadian healthy eating index (CHEI) in ulcerative colitis (UC) patients enrolled in a randomised controlled dietary intervention trial. Methods Patients with both active and quiescent disease were recruited from the Foothills Medical Center in Calgary, Alberta, Canada and randomised to either an 8-week reduced sulfur anti-inflammatory diet intervention (INT; n = 14) or conventional management control group (CM; n = 10). Each INT patient met with a registered dietitian for diet teaching, in person at baseline, over the phone at 2 weeks, and in person at 4 weeks. Stool samples and 24-h dietary recalls were collected at baseline and 8 weeks. DNA from stool samples was extracted and the V4 region of the 16S gene was sequenced. FCP was extracted and analyzed using the EK-CAL ELISA. An adapted CHEI was generated from diet recalls using previously validated scoring guidelines. Relationships between variables were analyzed using analysis of variance and chi-squared. Results Mean age of the sample was 36.3 (SD=8.7) and 58% were male. Baseline medications included aminosalicylates (71%), steroids (50%), biologics (33%), immunosuppressants (25%) and 21% of patients had taken antibiotics within the last 3 months. Α-diversity, or within-community diversity, significantly increased in the CM group and remained stable in the INT group over time (p = 0.005). Β-diversity, or between-community diversity appeared to increase in the intervention group over time (p < 0.01); however, this may have been influenced by antibiotic use in five patients. Significant differential features between the CM and INT groups (p < 0.01) at the genus level were identified in the phyla Firmicutes and Proteobacteria, specifically Catenibacterium, Parvimonas, Coprococcus_2 and Desulfovibrio. FCP appeared to be different between the groups (p = 0.05) with a greater percentage of INT patients moving from high FCP (>250 mg/g) to low FCP (<250 mg/g); 50% of INT patients and 20% of CM patients normalised FCP levels. As CHEI increased in the whole sample, indicating higher diet quality, FCP decreased significantly (p = 0.04). Conclusion In an interim analysis, a dietary intervention shows efficacy in manipulating the microbiome. Higher diet scores representing a healthier diet were also related to lower faecal calprotectin levels.