Background: Anxiety and mood disorders involve a high disease burden and are associated with high economic costs. A stepped-care approach intervention and abbreviated diagnostic method are assumed to increase effectiveness and efficiency of the mental healthcare and are expected to reduce economic costs. Methods: Presented are the rationale, design, and methods of a two-armed randomized controlled trial comparing 'treatment as usual' (TAU) with a brief intensified cognitive behavioral therapy (CBT) and/or pharmacotherapy. Eligible participants (N =500) of five Dutch outpatient Mental Healthcare Centers are randomly assigned to either TAU or to the experimental condition (brief CBT and/or pharmacotherapy). Data on patients' progress and clinical effectiveness of treatment are assessed at baseline, post-treatment (3. months after baseline), and at 6 and 12. months post-treatment by Routine Outcome Monitoring (ROM). Cost analysis is performed on the obtained data. Discussion: Since few studies have investigated both the clinical and cost effectiveness of a stepped-care approach intervention and a shortened diagnostic ROM method in both anxiety and/or mood disorders within secondary mental health care, the results of this study might contribute to the improvement of (cost)-effective treatment options and diagnostic methods for these disorders.