Abstract Female genital mutilation (FGM) has short and long-term impacts on the health of girls/women. In Portugal, an estimated 5246 women were subjected to it, with 568 of them residing in the city of Amadora, in the metropolitan area of the capital Lisbon. As such, Amadora was considered a priority area for developing strategies to prevent female genital mutilation, under the coordination of the local public health unit. Our aim was to capacitate professionals to recognise and act on risk/danger and on minimising potential health impacts of FGM on the local institutions these girls/women might come into contact with. We created a task force that held meetings with different local actors: hospital, teams at the primary healthcare facility, city hall of Amadora, child protection services, a school, social inclusion projects, representatives of the justice system and a non-governmental organisation. We designed different scenarios for the different needs and entry points of these girls/women in the system and created appropriate procedures for all these actors. Within the primary healthcare facility, we created guidelines specifying criteria for referral to other specialties. This led to the development of a county protocol targeting FGM during the summer of 2019. We trained 160 healthcare professionals. In addition, we created a booklet for schools and held sessions in school groups targeting teachers, psychologists and operational assistants with a focus on risk and danger indicators and on how to proceed. Overall, 360 school professionals received training. During these sessions, we also presented resources on how to integrate FGM in discussions with students regarding gender violence and human rights. This intervention will be evaluated after one year (summer of 2020) through mixed-methods to understand the impact on the practice of the professionals in Amadora. We will conduct interviews and apply questionnaires to capture the implementation of this city-wide protocol. Key messages Given the complexity of FGM a wide societal and multidisciplinary approach should be used with a public health team coordinating the intervention. In Portugal there is a need for an organised and systematic response by professionals regarding FGM; our county-specific protocol aimed to create that response.