Introduction: The Unified Protocol for Transdiagnostic Treatment of Emotional Disorders (UP) delivered in a group format could facilitate the implementation of evidence-based psychological treatments. Objective: This study compared the efficacy of group UP and diagnosis-specific cognitive behavioral therapy (dCBT) for anxiety and depression in outpatient mental health services. Methods: In this pragmatic, multi-center, single-blinded, non-inferiority, randomized controlled trial (RCT), we assigned 291 patients with major depressive disorder, social anxiety disorder, panic disorder, or agoraphobia to 14 weekly sessions in mixed-diagnosis UP or single-diagnosis dCBT groups. The primary test was non-inferiority, using a priori criteria, on the World Health Organisation 5 Well-Being Index (WHO-5) at the end of the treatment. Secondary outcomes were functioning and symptoms. We assessed outcomes at baseline, end-of-treatment, and at a 6-month follow-up. A modified per-protocol analysis was performed. Results: At end-of-treatment, WHO-5 mean scores for patients in UP (n = 148) were non-inferior to those of patients in dCBT (n = 143; mean difference -2.94; 95% CI -8.10 to 2.21). Results were inconclusive for the WHO-5 at the 6-month follow-up. Results for secondary outcomes were non-inferior at end-of-treatment and the 6-month follow-up. Client satisfaction and rates of attrition, response, remission, and deterioration were similar across conditions. Conclusions: This RCT demonstrated non-inferior acute-phase outcomes of group-delivered UP compared with dCBT for major depressive disorder, social anxiety disorder, panic disorder, and agoraphobia in outpatient mental health services. The long-term effects of UP on well-being need further investigation. If study findings are replicated, UP should be considered a viable alternative to dCBT for common anxiety disorders and depression in outpatient mental health services.