Migrants' overall health status may be improved by increasing the detection of certain infectious diseases and other conditions for which effective care is available. This can be achieved through a systematic screening of these conditions using innovative and digital solutions implemented in routine health care. This study aims to evaluate the implementation of a screening programme for migrants at primary care level in two different settings of Spain (Catalonia and Andalusia) using an innovative digital and user-friendly software tool (ISMiHealth). In Catalonia, the ISMiHealth tool has already been integrated into the Electronic Patient Record (EPR) system (eCAP) as part of a pilot study in 2018; currently, the research team aims to validate the tool in a higher number of primary care centres in this area. Therefore, a pragmatic cluster randomised controlled trial will be conducted with two parallel groups, in which selected centres using the novel software ISMiHealth will be compared to others that follow the current routine practice. On the other hand, in Andalusia a pilot cluster randomised controlled trial will be carried out, where the ISMiHealth tool will be implemented in the EPR system (DIRAYA) to evaluate the preliminary effectiveness of the tool in other settings. The ISMiHealth software is a clinical decision support system that provides recommendations for primary healthcare professionals on screening for targeted conditions. It currently includes: 7 communicable diseases (Human immunodeficiency virus, Hepatitis B and C virus, Tuberculosis, Chagas diseases, strongyloidiasis and schistosomiasis) and one key health condition (female genital mutilation). Through routinely collected variables (country of birth, age, and sex), the software performs an individualised risk assessment and provides real-time prompts to healthcare professionals on screening for the selected health conditions. In any case, health professionals will be responsible for requesting screening tests and/or referrals to specialists.