BACKGROUND: To promote well-being and health behaviors among adolescents, 2 interventions were implemented at 12 secondary schools. Adolescents in the E-health4Uth group received Web-based tailored messages focused on their health behaviors and well-being. Adolescents in the E-health4Uth and consultation group received the same tailored messages, but were subsequently referred to a school nurse for a consultation if they were at risk of mental health problems. OBJECTIVE: This study evaluated the effect of E-health4Uth and E-health4Uth and consultation on well-being (ie, mental health status and health-related quality of life) and health behaviors (ie, alcohol and drug use, smoking, safe sex). METHODS: A cluster randomized controlled trial was conducted among third- and fourth-year secondary school students (mean age 15.9, SD 0.69). School classes (clusters) were randomly assigned to (1) E-health4Uth group, (2) E-health4Uth and consultation group, or (3) control group (ie, care as usual). Adolescents completed a questionnaire at baseline and at 4-month follow-up assessing alcohol consumption, smoking, drug use, condom use, mental health via the Strengths and Difficulties Questionnaire (SDQ) and the Youth Self Report (YSR; only measured at follow-up), and health-related quality of life. Multilevel logistic, ordinal, and linear regression analyses were used to reveal differences in health behavior and well-being between the intervention groups and the control group at follow-up. Subsequently, it was explored whether demographics moderated the effects. RESULTS: Data from 1256 adolescents were analyzed. Compared to the control intervention, the E-health4Uth intervention, as a standalone intervention, showed minor positive results in health-related quality of life (B=2.79, 95% CI 0.72-4.87) and condom use during intercourse among adolescents of Dutch ethnicity (OR 3.59, 95% CI 1.71-7.55) not replicated in the E-health4Uth and consultation group. The E-health4Uth and consultation intervention showed minor positive results in the mental health status of adolescents (SDQ: B=-0.60, 95% CI -1.17 to -0.04), but a negative effect on drug use among boys (OR 0.36, 95% CI 0.13-0.96). In the subgroup of adolescents who were at risk of mental health problems at baseline (and referred for a consultation with the nurse), the E-health4Uth and consultation group showed minor to moderate positive results in mental health status (SDQ: B=-1.79, 95% CI -3.35 to -0.22; YSR: B=-9.11, 95% CI -17.52 to -0.71) and health-related quality of life (B=7.81, 95% CI 2.41-13.21) at follow-up compared to adolescents in the control group who were at risk of mental health problems at baseline. CONCLUSIONS: Findings from this study support the use of the E-health4Uth and consultation intervention in promoting the well-being of adolescents at risk of mental health problems. Future research is needed to further evaluate the effects of the consultation as a standalone intervention, and the dual approach of further tailored eHealth messages and a consultation. TRIAL REGISTRATION: Nederlands Trial Register: NTR 3596.