Introduction The long-term effectiveness of psychological interventions for the treatment of subthreshold depression and the prevention of depression is unclear and effects vary among subgroups of patients, indicating that not all patients profit from such interventions. Randomised clinical trials are mostly underpowered to examine adequately subgroups and moderator effects. The aim of the present study is, therefore, to examine the short-term and long-term as well as moderator effects of psychological interventions compared with control groups in adults with subthreshold depression on depressive symptom severity, treatment response, remission, symptom deterioration, quality of life, anxiety and the prevention of major depressive disorder (MDD) onsets on individual patient level and study level using an individual patient data meta-analysis approach. Methods and analysis Systematic searches in PubMed, PsycINFO, Embase and the Cochrane Central Register of Controlled Trials were conducted. We will use the following types of outcome criteria: (A) onset of major depression; (B) time to major depression onset; (C) observer-reported and self-reported depressive symptom severity; (D) response; (E) remission; (F) symptom deterioration; (G) quality of life, (H) anxiety; and (I) suicidal thoughts and behaviours. Multilevel models with participants nested within studies will be used. Missing data will be handled using a joint modelling approach to multiple imputation. A number of sensitivity analyses will be conducted in order test the robustness of our findings. Ethics and dissemination The investigators of the primary trials have obtained ethical approval for the data used in the present study and for sharing the data, if this was necessary, according to local requirements and was not covered from the initial ethic assessment. This study will summarise the available evidence on the short-term and long-term effectiveness of preventive psychological interventions for the treatment of subthreshold depression and prevention of MDD onset. Identification of subgroups of patients in which those interventions are most effective will guide the development of evidence-based personalised interventions for patients with subthreshold depression. PROSPERO registration number CRD42017058585.