Introduction Suicide is one of the leading public health issues worldwide. Mobile health can help us to combat suicide through monitoring and treatment. The SmartCrisis V.2.0 randomised clinical trial aims to evaluate the effectiveness of a smartphone-based Ecological Momentary Intervention to prevent suicidal thoughts and behaviour.Methods and analysis The SmartCrisis V.2.0 study is a randomised clinical trial with two parallel groups, conducted among patients with a history of suicidal behaviour treated at five sites in France and Spain. The intervention group will be monitored using Ecological Momentary Assessment (EMA) and will receive an Ecological Momentary Intervention called ‘SmartSafe’ in addition to their treatment as usual (TAU). TAU will consist of mental health follow-up of the patient (scheduled appointments with a psychiatrist) in an outpatient Suicide Prevention programme, with predetermined clinical appointments according to the Brief Intervention Contact recommendations (1, 2, 4, 7 and 11 weeks and 4, 6, 9 and 12 months). The control group would receive TAU and be monitored using EMA.Ethics and dissemination This study has been approved by the Ethics Committee of the University Hospital Fundación Jiménez Díaz. It is expected that, in the near future, our mobile health intervention and monitoring system can be implemented in routine clinical practice. Results will be disseminated through peer-reviewed journals and psychiatric congresses. Reference number EC005-21_FJD. Participants gave informed consent to participate in the study before taking part.Trial registration number CT04775160