Social prescribing (SP) is an intersectoral strategy of integrated care involving a link worker and multiple stakeholders to address users social, economic and emotional needs through the activation of community assets. SP can contribute to improve individuals’ health and well-being and strengthen health systems responsiveness and efficiency. Gaps remain about challenges and influencing factors of SP implementation process. This study assessed perceived barriers and facilitating strategies of implementation of a SP project in two Family Health Units in Lisbon. Semi-structured interviews were conducted with 9 stakeholders (family doctors, social workers and community partners involved in SP), exploring barriers and facilitators to SP planning and implementation. Data were analysed through content analysis technique based on the Consolidated Framework for Implementation Research domains. The main challenges in SP implementation described by participants were the insufficient human resources, lack of time from the link workers, lack of available community responses, and reduced user awareness and adherence to the intervention. Key facilitators of the intervention included knowing the community resources available and having the professionals qualified for the role of link worker. Strong engagement of general practitioners, health authorities and technicians from community sector, frequent communication between stakeholders, and physical presence of link workers at health services were also identified as facilitators. Furthermore, having a national commitment towards SP and the support of a trustworthy research team to monitor and evaluate SP implementation were highlighted. The settings specificities are crucial for the success of the SP, but they directly depend on both organisational and individual factors that change across contexts. Priority actions for effective implementation should focus on investments in training of health professionals and community partners and promotion of user adherence. These actions may contribute to maximising the SP benefits for improved integrated care, multisectoral collaborations, and health system strengthening and sustainability.