Background <p>Emotional disorders are the most prevalent mental health conditions worldwide. In Spain, the limited availability of mental health professionals has led to long waiting lists, contributing to the saturation of the Spanish National Health System (SNHS). This study protocol aims to evaluate the cost-effectiveness and acceptability of the Unified Protocol delivered in group format, using two brief versions (5 and 8 sessions), through a randomized controlled trial in Primary Care centers across Spain. The study also aims to identify patient profiles responding better to each condition.</p> Method <p>Participants diagnosed with emotional disorders will be randomly assigned (1:1 ratio) to the 5- or 8-session Unified Protocol condition. Randomization will be stratified by severity of anxiety and depressive symptoms. A minimum of 180 participants will be recruited. Assessments will be conducted up to the 6-month follow-up. Data will be analyzed using descriptive statistics, Pearson’s <i>r</i> correlations, multiple linear regressions, <i>t</i>-tests, repeated measures ANOVA, hierarchical models, cross lagged panel models and effect size calculations (Cohen’s <i>d</i>). The results of this study will explore the cost-effectiveness, and acceptability of the two brief Unified Protocol formats, as well as identify patient profiles that benefit most from each version.</p> Discussion <p>Findings could improve access to evidence-based care, reduce waiting lists and identify patient profiles to guide personalized, efficient interventions while optimizing SNHS resources.</p> Trial registration <p>Clinical Trial Number (NCT06547450||<a href="https://clinicaltrials.gov/study/NCT06547450">https://clinicaltrials.gov/study/NCT06547450</a>) with the Clinical Trial Registry (7^th August 2024).</p>