Background Patient education, home-based exercise therapy, and advice on returning to normal activities are established physiotherapeutic treatment options for patients with nonspecific low back pain (LBP). However, the effectiveness of physiotherapy interventions on health-related outcomes largely depends on patient self-management and adherence to exercise and physical activity recommendations. e-Exercise LBP is a recently developed stratified blended care intervention comprising a smartphone app integrated with face-to-face physiotherapy treatment. Following the promising effects of web-based applications on patients’ self-management skills and adherence to exercise and physical activity recommendations, it is hypothesized that e-Exercise LBP will improve patients’ physical functioning. Objective This study aims to investigate the short-term (3 months) effectiveness of stratified blended physiotherapy (e-Exercise LBP) on physical functioning in comparison with face-to-face physiotherapy in patients with nonspecific LBP. Methods The study design was a multicenter cluster randomized controlled trial with intention-to-treat analysis. Patients with nonspecific LBP aged ≥18 years were asked to participate in the study. The patients were treated with either stratified blended physiotherapy or face-to-face physiotherapy. Both interventions were conducted according to the Dutch physiotherapy guidelines for nonspecific LBP. Blended physiotherapy was stratified according to the patients’ risk of developing persistent LBP using the Keele STarT Back Screening Tool. The primary outcome was physical functioning (Oswestry Disability Index, range 0-100). Secondary outcomes included pain intensity, fear-avoidance beliefs, and self-reported adherence. Measurements were taken at baseline and at the 3-month follow-up. Results Both the stratified blended physiotherapy group (104/208, 50%) and the face-to-face physiotherapy group (104/208, 50%) had improved clinically relevant and statistically significant physical functioning; however, there was no statistically significant or clinically relevant between-group difference (mean difference −1.96, 95% CI −4.47 to 0.55). For the secondary outcomes, stratified blended physiotherapy showed statistically significant between-group differences in fear-avoidance beliefs and self-reported adherence. In patients with a high risk of developing persistent LBP (13/208, 6.3%), stratified blended physiotherapy showed statistically significant between-group differences in physical functioning (mean difference −16.39, 95% CI −27.98 to −4.79) and several secondary outcomes. Conclusions The stratified blended physiotherapy intervention e-Exercise LBP is not more effective than face-to-face physiotherapy in patients with nonspecific LBP in improving physical functioning in the short term. For both stratified blended physiotherapy and face-to-face physiotherapy, within-group improvements were clinically relevant. To be able to decide whether e-Exercise LBP should be implemented in daily physiotherapy practice, future research should focus on the long-term cost-effectiveness and determine which patients benefit most from stratified blended physiotherapy. Trial Registration ISRCTN Registry 94074203; https://doi.org/10.1186/ISRCTN94074203 International Registered Report Identifier (IRRID) RR2-https://doi.org/10.1186/s12891-020-3174-z