Background Depression and anxiety are common and co-morbid disorders that affect a significant proportion of students. Innovative prevention strategies targeting both conditions are needed to reduce their health burden and costs. ICare Prevent is such an innovative strategy and contains a transdiagnostic individually tailored Internet-based and mobile-supported intervention. It addresses common risk factors of depression and anxiety as part of a large EU-funded multi-country project* (ICare). Little is known about the clinical and cost-effectiveness of this type of intervention compared to care as usual (CAU) for college students. We hypothesize that ICare Prevent will be more (cost-)effective than CAU in the reduction of symptoms of depression and anxiety. Methods A three-arm, parallel, randomized controlled superiority trial will be conducted comparing a guided and an unguided version of ICare Prevent with a control group receiving CAU. The trial will be open-label but outcome assessors will be blinded. A total of 252 college students (age ≥ 16 years) with subclinical symptoms of depression defined as a score ≥ 16 on the Center for Epidemiological Studies Depression Scale (CES-D), and/or anxiety, defined as a score ≥ 5 on the Generalized Anxiety Disorder scale (GAD-7), will be included. Those meeting diagnostic criteria for a depressive or anxiety disorder will be excluded. The primary outcome is change in disorder specific symptom severity from baseline to post-intervention. Secondary endpoints include self-reported depression and anxiety symptoms as well as time to onset of a mood or anxiety disorder until 12-month follow-up. Societal costs and quality of life will be assessed to estimate the intervention’s cost-effectiveness compared to CAU. Discussion Transdiagnostic individually tailored Internet-based prevention could be a (cost-)effective approach to tackle the disease burden of depression and anxiety among college students. Trial registration Dutch trial register, NTR 6562. Registered on 6 July 2017.