Objective To investigate the effectiveness of a multi-facetted blended eHealth intervention, called SDM-Digital Intake (SDM-DI), in which patients and clinicians are supported in Shared Decision Making during the intake process. Methods The study is a two-arm matched-paired cluster Randomised Controlled Trial in a specialist mental health outpatient setting with two conditions: SDM-DI and Intake As Usual (IAU). Four intake teams were allocated to each arm. All patients who followed an intake, were asked to participate if they were capable to complete questionnaires. Decisional Conflict (DC), referring to patients’ engagement and satisfaction with clinical decisions, was the primary outcome. Secondary outcomes were patient participation, applying Shared Decision Making (SDM), working alliance, treatment adherence and symptom severity. Effects were measured at two weeks (T1) and two months (T2) after intake. Multilevel regression and intention-to-treat analyses were used. Additionally, the influence of subgroups and intervention adherence on DC were explored. Results At T1, 200 patients participated (47% intervention, 53% control), and at T2 175 patients (47% intervention, 53% control). At T1 and T2, no differences were found between conditions on DC. Subgroup analyses showed that effects of SDM-DI on DC were not modified by primary diagnoses mood, anxiety and personality disorders. Compared to IAU, at T2, patients reported positive effects of SDM-DI on SDM (β 7.553, p = 0.038, 95%CI:0.403–14.703, d = 0.32) and reduction of symptoms (β -7.276, p = 0.0497, 95%CI:-14.544–-0.008, d = -0.43). No effects were found on patient participation, working alliance and treatment adherence. Exploratory analyses demonstrated that if SDM was applied well, patients reported less DC (β = -0.457, p = 0.000, 95%CI:-0.518–-0.396, d = -1.31), which was associated with better treatment outcomes. Conclusion Although, this trial fails to demonstrate that SDM-DI by itself is sufficient to reduce DC, the results are encouraging for further efforts in improving and implementing the SDM intervention.