Objective: Inflammatory bowel disease (IBD) is characterized by a low level of quality of life (QoL) and a high prevalence of anxiety and depression, especially in patients with poor QoL. We examined the effect of IBD-specific cognitive–behavioral therapy (CBT) on QoL, anxiety, and depression in IBD patients with poor mental QoL. Method: This study is a parallel-group multicenter randomized controlled trial. One hundred eighteen IBD patients with a low level of QoL (score ≤23 on the mental health subscale of the Medical Outcomes Study Short Form 36 Health Survey [SF-36]) were included from 2 academic medical centers (Academic Medical Center Amsterdam, VU University Medical Centre Amsterdam) and 2 peripheral medical centers (Flevo Hospital, Slotervaart Hospital) in the Netherlands. Patients were randomized to an experimental group receiving CBT (n = 59) versus a wait-list control group (n = 59) receiving standard medical care for 3.5 months, followed by CBT. Both groups completed baseline and 3.5 months follow-up assessments. The primary outcome was a self-report questionnaire and disease-specific QoL (Inflammatory Bowel Disease Questionnaire [IBDQ]). Secondary outcomes were depression (Hospital Anxiety and Depression Scale–Depression Subscale [HADS-D], Center for Epidemiologic Studies Depression Scale [CES-D]), anxiety (HADS–Anxiety Subscale [HADS-A]) and generic QoL (SF-36). Results: Data were analyzed both on intention to treat as well as on per protocol analysis (completed ≥5 sessions). CBT had a positive effect on disease-specific-QoL (Cohen’s d = .64 for IBDQ total score), depression (Cohen’s d = .48 for HADS-D and .78 for CES-D), anxiety (Cohen’s d = .58 for HADS-A), and generic QoL (Cohen’s d = 1.08 for Mental Component Summary of the SF-36; all ps < .01). Conclusions: IBD-specific CBT is effective in improving QoL and in decreasing anxiety and depression in IBD patients with poor QoL. Clinicians should incorporate screening on poor mental QoL and consider offering CBT.