Abstract Background Emotional disorders are common, and they have become more prevalent since the COVID-19 pandemic. Due to a high attendance burden at the specialized level, most emotional disorders in Spain are treated in primary care, where they are usually misdiagnosed and treated using psychotropic drugs. This contributes to perpetuate their illness and increase health care costs. Following the IAPT programme and the transdiagnostic approach, the PsicAP project developed a brief group transdiagnostic cognitive-behavioural therapy (tCBT) as a cost-effective alternative. However, it is not suitable for everyone; in some cases, one-on-one sessions may be more effective. The objective of the present study is to compare, in cost-benefit terms, group and individual tCBT with the treatment usually administered in Spanish primary care (TAU). Methods A randomized, controlled, multicentre, and single-blinded trial will be performed. Adults with mild to moderate emotional disorders will be recruited and placed in one of three arms: group tCBT, individual tCBT, or TAU. Medical data and outcomes regarding emotional symptoms, disability, quality of life, and emotion regulation biases will be collected at baseline, immediately after treatment, and 6 and 12 months later. The data will be used to calculate incremental cost-effectiveness and cost-utility ratios. Discussion This trial aims to contribute to clinical practice research. The involvement of psychologists in primary care and the implementation of a stepped-care model for mental disorders are recommended. Group therapy and a transdiagnostic approach may help optimize health system resources and unblock waiting lists so that people can spend less time experiencing mental health problems. Trial registration ClinicalTrials.gov: NCT04847310; Protocols.io: bx2npqde. (April 19, 2021)