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Introduction Youth in remission of depression or anxiety have high risks of relapse. Relapse prevention interventions may prevent chronicity. Aim of the study is therefore to (1) examine efficacy of the personalised StayFine app for remitted youth and (2) identify high-risk groups for relapse and resilience.Method and analysis In this Dutch single-blind parallel-group randomised controlled trial, efficacy of app-based monitoring combined with guided app-based personalised StayFine intervention modules is assessed compared with monitoring only. In both conditions, care as usual is allowed. StayFine modules plus monitoring is hypothesised to be superior to monitoring only in preventing relapse over 36 months. Participants (N=254) are 13–21 years and in remission of depression or anxiety for >2 months. Randomisation (1:1) is stratified by previous treatment (no treatment vs treatment) and previous episodes (1, 2 or >3 episodes). Assessments include diagnostic interviews, online questionnaires and monitoring (ecological momentary assessment with optional wearable) after 0, 4, 12, 24 and 36 months. The StayFine modules are guided by certified experts by experience and based on preventive cognitive therapy and ingredients of cognitive behavioural therapy. Personalisation is based on shared decision-making informed by baseline assessments and individual symptom networks. Time to relapse (primary outcome) is assessed by the Kiddie Schedule for Affective Disorders and Schizophrenia-lifetime version diagnostic interview. Intention-to-treat survival analyses will be used to examine the data. Secondary outcomes are symptoms of depression and anxiety, number and duration of relapses, global functioning, and quality of life. Mediators and moderators will be explored. Exploratory endpoints are monitoring and wearable outcomes.Ethics, funding and dissemination The study was approved by METC Utrecht and is funded by the Netherlands Organisation for Health Research and Development (636310007). Results will be submitted to peer-reviewed scientific journals and presented at (inter)national conferences.Trial registration number NCT05551468; NL8237.