--- - |2+ Abstract Objective Anxiety and depression are common in inflammatory bowel disease (IBD) and have been linked to clinical recurrence. Previous randomized controlled trials (RCT's) have found no evidence that psychological interventions enhance outcomes for people with IBD but have recruited patients without distress. This study investigates the clinical benefits of a nonrandomized uncontrolled study of clinic based cognitive behaviour therapy (CBT) for people with IBD who had moderate–severe levels of anxiety or low mood and compares the results with a previous RCT of CBT in this population. Method Assessments were completed at baseline and end of treatment and included measures of low mood, generalized anxiety, quality of life (QOL), and symptomatic disease activity. The patient health questionnaire and generalized anxiety disorder 7 measures were the primary outcomes. Results in the form of a standardized effect size of treatment were compared with a previous RCT to consider if CBT had greater benefits for those with distress. Results Thirty patients were deemed appropriate for CBT, and 28 accepted treatment. The results from this clinic based CBT intervention suggest statistically significant reductions in symptoms of anxiety (<0.001), low mood (<0.001), and disease activity (p < 0.01) and increases in QOL (p < 0.001). The uncontrolled effect sizes were large and superior to those found in published RCTs. Conclusion This nonrandomized uncontrolled trial of a clinic‐based CBT intervention suggests that CBT may have benefits for those with moderate–severe disturbances to mood and that effect sizes can be improved by targeting those with distress. RCTs are required to establish efficacy. - Clinical Psychology & Psychotherapy, EarlyView.