Background: Patient education, advice on returning to normal activities and (home-based) exercise therapy are established treatment options for patients with non-specific low back pain (LBP). However, the effectiveness of physiotherapy interventions on physical functioning and prevention of recurrent events largely depends on patient self-management, adherence to prescribed (home-based) exercises and recommended physical activity behaviour. Therefore we have developed e-Exercise LBP, a blended intervention in which a smartphone application is integrated within face-to-face care. E-Exercise LBP aims to improve patient self-management skills and adherence to exercise and physical activity recommendations and consequently improve the effectiveness of physiotherapy on patients' physical functioning. The aim of this study is to investigate the short- (3 months) and long-term (12 and 24 months) effectiveness on physical functioning and cost-effectiveness of e-Exercise LBP in comparison to usual primary care physiotherapy in patients with LBP. Methods: This paper presents the protocol of a prospective, multicentre cluster randomized controlled trial. In total 208 patients with LBP pain were treated with either e-Exercise LBP or usual care physiotherapy. E-Exercise LBP is stratified based on the risk for developing persistent LBP. Physiotherapists are able to monitor and evaluate treatment progress between face-to-face sessions using patient input from the smartphone application in order to optimize physiotherapy care. The smartphone application contains video-supported self-management information, video-supported exercises and a goal-oriented physical activity module. The primary outcome is physical functioning at 12-months follow-up. Secondary outcomes include pain intensity, physical activity, adherence to prescribed (home-based) exercises and recommended physical activity behaviour, self-efficacy, patient activation and health-related quality of life. All measurements will be performed at baseline, 3, 12 and 24 months after inclusion. An economic evaluation will be performed from the societal and the healthcare perspective and will assess cost-effectiveness of e-Exercise LBP compared to usual physiotherapy at 12 and 24 months. Discussion: A multi-phase development and implementation process using the Center for eHealth Research Roadmap for the participatory development of eHealth was used for development and evaluation. The findings will provide evidence on the effectiveness of blended care for patients with LBP and help to enhance future implementation of blended physiotherapy. Trial registration: ISRCTN, ISRCTN94074203. Registered 20 July 2018 - Retrospectively registered.