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Abstract Background Data from primary health care in Spain show a high prevalence of the major depressive disorder. Blended treatment (combination of face-to-face and online components) seems to be a very promising tool for the optimization and dissemination of psychological treatments in a cost-effective form. Although there is growing data that confirm the advantages of blended therapies, few studies have analyzed their application in regular clinical practice. The objective of the present paper is to describe the protocol for a clinical study aimed at exploring the clinical and cost-effectiveness of a blended cognitive behavioral therapy (b-CBT) for depression, compared to treatment as usual (TAU) in a primary health care setting. Methods A two-arm randomised controlled non-inferiority trial will be carried out, with repeated measures (baseline, 3 months, 6 months, and 12 months) under two conditions: b-CBT and TAU. The b-CBT program will consist in three face-to-face sessions and eight online sessions. The TAU is defined as the routine care delivered by the general practitioner for the treatment of depression in primary care. The primary outcome is a symptomatic change of depressive symptoms on the patient-health questionnaire (PHQ-9). Other secondary outcomes will be considered (e.g., quality of life, treatment preference). All participants must be 18 years of age or older and meet the diagnostic criteria for major depressive disorder according to the Diagnostic and Statistical Manual of Mental disorders 4th edition. 156 participants will be recruited (78 per arm). Discussion It is expected that b-CBT is clinically non-inferior when compared to TAU. This is the first study in Spain to use a b-CBT format in primary and specialized care, and this format could be an efficacious and cost-effective therapeutic strategy for the treatment of depression. Trial registration ClinicalTrials.gov NCT02361684. Registered on 8 January 2015. Currently recruiting participants.