The Syrian crisis, followed by a financial crisis, port explosion, and COVID-19, have put enormous strain on Lebanon’s health system. Syrian refugees and the vulnerable host population have a high burden of Non-communicable Diseases (NCD) morbidity and unmet mental health, psychosocial and rehabilitation needs. The International Committee of the Red Cross (ICRC) recently introduced integrated NCD services within its package of primary care in Lebanon, which includes NCD primary health care, rehabilitation, and mental health and psychosocial support services. We aimed to identify relevant outcomes for people living with NCDs from refugee and host communities in northern Lebanon, as well as to define the processes needed to achieve them through an integrated model of care. Given the complexity of the health system in which the interventions are delivered, and the limited practical guidance on integration, we considered systems thinking to be the most appropriate methodological approach.