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Introduction ISMiHealth is a clinical decision support system, integrated as a software tool in the electronic health record system of primary care, that aims to improve the screening performance on infectious diseases and female genital mutilation (FGM) in migrants. The aim of this study is to assess the health impact of the tool and to perform a process evaluation of its feasibility and acceptability when implemented in primary care in Catalonia (Spain).Methods and analysis This study is a cluster randomised control trial where 35 primary care centres in Catalonia, Spain will be allocated into one of the two groups: intervention and control. The health professionals in the intervention centres will receive prompts, through the ISMiHealth software, with screening recommendations for infectious diseases and FGM targeting the migrant population based on an individualised risk assessment. Health professionals of the control centres will follow the current routine practice.A difference in differences analysis of the diagnostic rates for all aggregated infections and each individual condition between the intervention and control centres will be performed. Mixed-effects logistic regression models will be carried out to identify associations between the screening coverage and predictor factors. In addition, a process evaluation will be carried out using mixed methodology.Ethics and dissemination The study protocol has been approved by the institutional review boards at Hospital Clínic (16 June 2022, HCB/2022/0363), Clinical Research Ethics Committee of the Primary Care Research Institute IDIAPJGol (22 June 2022, 22/113-P) and the Almería Research Ethics Committee (27 July 2022, EMC/apg). The study will follow the tenets of the Declaration of Helsinki and Good Clinical Practice. All researchers and associates signed a collaboration agreement in which they undertake to abide by good clinical practice standards.Findings will be disseminated in peer-reviewed journals and communications to congresses.Trial registration number NCT05868005.