Obesity is currently becoming a serious global public health problem due to its high prevalence and continuous increase. This condition is associated with different physical and mental health problems. The presence of emotional disorders (anxiety, depression and related disorders) among candidates for bariatric surgery is very high and predicts worse physical and psychological results. The present study aims to explore the feasibility and clinical usefulness of the Unified Protocol, a transdiagnostic emotion regulation-based intervention, delivered in an online group format to patients with emotional disorder diagnosis or symptoms, who are waiting for bariatric surgery. We will conduct a pilot study with a repeated single-case experimental design (multiple baseline design) in a public mental health service. The sample will consist of 60 participants, who will be randomized to three baseline conditions: 8, 12 or 15 evaluation days before the intervention. Diagnostic criteria, symptomatology and body mass index are the primary outcome measures, and we will include affectivity, personality, quality of life, body image, eating behavior and surgical complications like secondary measures. An analysis of treatment satisfaction will be also performed. Assessment points will include pre-treatment, baseline, treatment, post-treatment, and follow-ups every three months until two years after post-treatment. The results obtained in this study may have important clinical, social and economic implications for public mental health.