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.