IntroductionThe health burden due to depression is ever increasing in the world. Prevention is a key to reducing this burden. Guided internet cognitive–behavioural therapies (iCBT) appear promising but there is room for improvement because we do not yet know which of various iCBT skills are more efficacious than others, and for whom. In addition, there has been no platform for iCBT that can accommodate ongoing evolution of internet technologies.Methods and analysisBased on our decade-long experiences in developing smartphone CBT apps and examining them in randomised controlled trials, we have developed the Resilience Training App Version 2. This app now covers five CBT skills: cognitive restructuring, behavioural activation, problem-solving, assertion training and behaviour therapy for insomnia. The current study is designed as a master protocol including four 2×2 factorial trials using this app (1) to elucidate specific efficacies of each CBT skill, (2) to identify participants’ characteristics that enable matching between skills and individuals, and (3) to allow future inclusion of new skills. We will recruit 3520 participants with subthreshold depression and ca 1700 participants without subthreshold depression, to examine the short-term efficacies of CBT skills to reduce depressive symptoms in the former and to explore the long-term efficacies in preventing depression in the total sample. The primary outcome for the short-term efficacies is the change in depressive symptoms as measured with the Patient Health Questionnaire-9 at week 6, and that for the long-term efficacies is the incidence of major depressive episodes as assessed by the computerised Composite International Diagnostic Interview by week 50.Ethics and disseminationThe trial has been approved by the Ethics Committee of Kyoto University Graduate School of Medicine (C1556).Trial registration numberUMIN000047124.