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Introduction Evidence-based and scalable prevention and promotion focused mental health and psychosocial support interventions are needed for conflict-affected populations in humanitarian settings. This study retrospectively assessed whether participation in Self Help Plus (SH+) versus enhanced usual care (EUC) resulted in reduced incidence of probable mental disorder and increased positive mental health and well-being post-intervention among South Sudanese refugee women in Uganda.Methods This study used secondary data from treatment-oriented pilot (n=50) and fully-powered cluster randomised controlled trials (cRCT)s (n=694) of SH+ versus EUC. Data from baseline and post-intervention assessments were combined. A composite latent indicator for mental health problems was generated using mental health and well-being measures included in both cRCTs. In order to assess incidence, a binary variable approximating probable mental disorder was created to exclude those with probable mental disorder from the analysis sample and as the primary prevention outcome. The promotive effects of SH+ relative to EUC were examined in the same sample by assessing subjective well-being and psychological flexibility scale scores.Results A single factor for mental health problems was identified with all factor loadings >0.30 and acceptable internal consistency (α=0.70). We excluded 161 women who met criteria for probable mental disorder at baseline. Among those with at least moderate psychological distress but without probable mental disorder at baseline and with follow-up data (n=538), the incidence of probable mental disorder at post-intervention was lower among those who participated in SH+ relative to EUC (Risk ratio =0.16, 95% CI: 0.05 to 0.53). Participation in SH+ versus EUC was also associated with increased subjective well-being (β=2.62, 95% CI: 1.63 to 3.60) and psychological flexibility (β=4.55, 95% CI: 2.92 to 6.18) at post-intervention assessment.Conclusions These results support the use and further testing of SH+ as a selective and indicated prevention and promotion focused psychosocial intervention in humanitarian settings.Trial registration number ISRCTN50148022.